date:20091202


rkevinbur...@charter.net wrote:

If I have data that I feed into shapio.test and jarque.bera.test yet they seem 
to disagree. What do I use for a decision?


I feel those testing for normality in real applied work always have some 
masochistic attitude. This attitude is squared if they/you even try out 
a second test. There are three possible results:


1. Both tests do not reject: You still do not know if the underlying 
distribution is normal. Hence a useless result.


2. Both tests do reject: You know with some probability 1-\alpha that 
your data are not normal but you do not know what to do next now - 
except for things that are obvious when looking at you data - and you 
should have done that before the analysis anyway. If nothing was obvious 
before, you will hide your finding about the non-normality now - or use 
another method that might be less powerful given the difference from 
normality is not really big.


3. Your case, one test rejects, the other one not: Welcome, you finally 
arrived in hell.



Best wishes,
Uwe Ligges








For my data set I have p.value of 0.05496421 returned from the shapiro.test and 
0.882027 returned from the jarque.bera.test. I have included the data set below.

Thank you.

Kevin


Category,Period,Residual
CHILD HATS, WIGS  MASKS,1/1/2005,-0.449735723758323
CHILD HATS, WIGS  MASKS,2/1/2005,0.281461045050074
CHILD HATS, WIGS  MASKS,3/1/2005,0.591383050911335
CHILD HATS, WIGS  MASKS,4/1/2005,0.239998659520616
CHILD HATS, WIGS  MASKS,5/1/2005,0.00343879474063987
CHILD HATS, WIGS  MASKS,6/1/2005,-2.64372061292663
CHILD HATS, WIGS  MASKS,7/1/2005,0.381630655290173
CHILD HATS, WIGS  MASKS,8/1/2005,-1.79543281552347
CHILD HATS, WIGS  MASKS,9/1/2005,1.90631012440313
CHILD HATS, WIGS  MASKS,10/1/2005,-0.256232543929779
CHILD HATS, WIGS  MASKS,11/1/2005,1.83452602676812
CHILD HATS, WIGS  MASKS,12/1/2005,-1.06869719416837
CHILD HATS, WIGS  MASKS,1/1/2006,1.04378655286183
CHILD HATS, WIGS  MASKS,2/1/2006,0.232655831328322
CHILD HATS, WIGS  MASKS,3/1/2006,-0.939084802643773
CHILD HATS, WIGS  MASKS,4/1/2006,0.854132879285335
CHILD HATS, WIGS  MASKS,5/1/2006,-1.71217066877156
CHILD HATS, WIGS  MASKS,6/1/2006,1.28040273099582
CHILD HATS, WIGS  MASKS,7/1/2006,-0.386415431325857
CHILD HATS, WIGS  MASKS,8/1/2006,-0.769127669783483
CHILD HATS, WIGS  MASKS,9/1/2006,-0.810996835089867
CHILD HATS, WIGS  MASKS,10/1/2006,0.0477292147635991
CHILD HATS, WIGS  MASKS,11/1/2006,0.294672848750557
CHILD HATS, WIGS  MASKS,12/1/2006,-0.0841330473924862
CHILD HATS, WIGS  MASKS,1/1/2007,0.231663729192233
CHILD HATS, WIGS  MASKS,2/1/2007,-0.601790650547443
CHILD HATS, WIGS  MASKS,3/1/2007,0.285635768516625
CHILD HATS, WIGS  MASKS,4/1/2007,-0.963154959558619
CHILD HATS, WIGS  MASKS,5/1/2007,1.52188112949994
CHILD HATS, WIGS  MASKS,6/1/2007,-0.826092842933196
CHILD HATS, WIGS  MASKS,7/1/2007,1.91937201229077
CHILD HATS, WIGS  MASKS,8/1/2007,-0.317789483136924
CHILD HATS, WIGS  MASKS,9/1/2007,-0.865011007394312
CHILD HATS, WIGS  MASKS,10/1/2007,-0.0281604973711276
CHILD HATS, WIGS  MASKS,11/1/2007,-0.123887049811822
CHILD HATS, WIGS  MASKS,12/1/2007,-0.0327727730592468
CHILD HATS, WIGS  MASKS,1/1/2008,-0.0654939600771254
CHILD HATS, WIGS  MASKS,2/1/2008,0.279247739913908
CHILD HATS, WIGS  MASKS,3/1/2008,0.167606602923418
CHILD HATS, WIGS  MASKS,4/1/2008,0.189533097427477
CHILD HATS, WIGS  MASKS,5/1/2008,0.402062194225847
CHILD HATS, WIGS  MASKS,6/1/2008,1.97150984262995
CHILD HATS, WIGS  MASKS,7/1/2008,-2.27538477532968
CHILD HATS, WIGS  MASKS,8/1/2008,1.89091792097945
CHILD HATS, WIGS  MASKS,9/1/2008,0.0251732151287081
CHILD HATS, WIGS  MASKS,10/1/2008,-0.2349741808124
CHILD HATS, WIGS  MASKS,11/1/2008,-0.659332058368173
CHILD HATS, WIGS  MASKS,12/1/2008,0.127284768034285
CHILD HATS, WIGS  MASKS,1/1/2009,-1.42838560676513
CHILD HATS, WIGS  MASKS,2/1/2009,0.617689775286461
CHILD HATS, WIGS  MASKS,3/1/2009,-0.034243005247084
CHILD HATS, WIGS  MASKS,4/1/2009,-0.304574261133836
CHILD HATS, WIGS  MASKS,5/1/2009,0.128679369916751
CHILD HATS, WIGS  MASKS,6/1/2009,-0.657479389968652
CHILD HATS, WIGS  MASKS,7/1/2009,0.608766068692517
CHILD HATS, WIGS  MASKS,8/1/2009,1.92814770869400
CHILD HATS, WIGS  MASKS,9/1/2009,-0.172644961366165
CHILD HATS, WIGS  MASKS,10/1/2009,-0.453255508263169
CHILD HATS, WIGS  MASKS,11/1/2009,-1.09903330959344

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[R] Again on overlaying plots (a plot region within a plot region)

2009-12-02 Thread Charlotte Maia

Hi Ottorino-Luca,

I'm not sure how flexible the layout command is off the top of my head.
I have never seen an example of what you describe using layout, so I
will assume it can't be done.

One option is to use grid and lattice.
This is possibly the best option if you are planning to do a lot of
this sort of thing.

Another option is to plot the second plot, on top of the first plot,
using primitives such as points and lines, transforming your
coordinates so that they match the coordinates of the first plot. This
will be very difficult if you wish to put titles and axis on the
nested plot, however simple if you restrict yourself to points and
lines. Finding documentation and examples of R's graphical primitives
should be easy.

At the risk of sounding crude, I'm pretty sure both latex and many
word processors allow one position one figure on top of another. This
would seem the simplest solution for a one off job.

Further to my post on R-devel, I recommend not using png format,
except where absolutely necessary.

regards
-- 
Charlotte Maia
http://sites.google.com/site/maiagx/home

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Re: [R] R script From PHP

I tried calling R from a shell script and it works. This is an example file
rscript.sh

R --no-save  EOT
x-2*pi
print(cbind(x,sin(x)))
quit(no)
EOT

This works perfectly on the Linux machine in which I have logged in via SSH
using the command (./rscript.sh)

I tried running this command using php

html
?php

$output = array();
$$retval = 0;
$a = shell_exec('./rscript.sh'. 21);
//print phpinfo();
print $a;

?
/html

this does not work and gives me this error:

./rscript.sh: line 1: R: command not found

Anybody familiar with this?

On Tue, Dec 1, 2009 at 5:35 PM, Romain Francois
romain.franc...@dbmail.comwrote:

 On 12/01/2009 12:48 PM, Hrishi Mittal wrote:

 Hi Amrit,

 I believe you can you use the PHP system command to call Rscript or R CMD.
 I
 don't know much PHP but this page might be useful -
 http://php.net/manual/en/function.system.php.

 You might also want to look at rapache -
 http://biostat.mc.vanderbilt.edu/rapache/

 Good luck with your project and do post a link to your webpage when you
 get
 it running.


 There is also a simple php client to Rserve in the next version of Rserve.
 http://www.rforge.net/Rserve/index.html

 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
 `- http://tr.im/BcPw : celebrating R commit #5



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Re: [R] Problem with Cannot compute correct p-values with ties

2009-12-02 Thread Karl Ove Hufthammer

On Wed, 02 Dec 2009 16:52:23 +0800 Zhijiang Wang 
ivoryto...@emails.bjut.edu.cn wrote:
Dear All,
1. why did the problem happen?
2. How to solve it?

A good start would be to follow the advice at the bottom of every 
posting on this mailing list:

PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

-- 
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[R] RWeka problem with WrapperSubsetEval

2009-12-02 Thread Itziar Frades Alzueta

Dear all,



I am trying to construct a wrapper that uses random forest to evaluate
the subsets using RWeka and when I do:



nombi - make_Weka_filter(weka/attributeSelection/WrapperSubsetEval)

datbin- nombi(gene ~., data=X1X2X3X4W,  control =Weka_control( B =
list(weka.classifiers.trees.RandomForest)))



I also have tried with an other induction algorithm:

datbin- nombi(gene ~., data=X1X2X3X4W,  control =Weka_control(
B=list(weka.classifiers.trees.j48.J48 -F 5 -T 0.01 -S 1 -- -C 0.25 -M
2)))



and in both cases I get the following error:



Error in .jcall(filter, Z, setInputFormat, instances) :

  method setInputFormat with signature (Lweka/core/Instances;)Z not
found



Thanks in advance,

Itziar Frades


 

 

 



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Re: [R] Problem with Cannot compute correct p-values with ties

Please try to find answers by yourself
You should not just post problems without thinking them.

 Huang, Guo-Hao

--
From: Zhijiang Wang ivoryto...@emails.bjut.edu.cn
Sent: Wednesday, December 02, 2009 4:52 PM
To: R-help@r-project.org
Subject: [R] Problem with Cannot compute correct p-values with ties

   Dear All,
   1. why did the problem happen?
   2. How to solve it?

   --

Best wishes,
Zhijiang Wang

PHD Student
Room 212, Science buliding,
The International WIC Institute,
College of Computer Science and Technology,
Beijing University of Technology,
Beijing, China.
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Re: [R] lattice: adding information on number of observations

2009-12-02 Thread Felix Andrews

Depends on exactly how / where you want to display the text.

One approach (showing text inside each panel, at the bottom):

bwplot(val ~ grp | panvar, data = dat,
  panel = function(x, y, ...) {
panel.bwplot(x, y, ...)
nn - table(x)
panel.text(paste(n =, nn), x = seq_along(nn),
   y = current.panel.limits()$y[1], pos = 3)
  })


2009/12/2 RINNER Heinrich heinrich.rin...@tirol.gv.at:
 Dear R-users,

 I am using R version 2.9.1 and lattice 0.17-26 under windows.
 In a lattice boxplot, I would like to add information on how many 
 observations each singel boxplot is based upon.

 For example (the basic plot):
 # Begin R-code
 library(lattice)
 dat - data.frame(panvar = rep(c(A,B,A,B), c(3,7,4,6)), grp = 
 rep(c(grp1, grp2), c(10,10)), val = rnorm(20))
 dat
 bwplot(val ~ grp | panvar, data = dat)
 # End R-code

 As in my real life data the number of observations in each subgroup will be 
 quite different, I would like to include the number of observations each 
 boxplot is based upon.
 Aggregation will tell me the numbers:
 # Begin R-code
 aggregate(dat$val, by = list(dat$panvar, dat$grp), FUN = length)
 # End R-code
 But how to match these numbers with the plot (so that for example n=3 will 
 be written as text beneath panel A/group1)?

 Any advice would be appreciated;
 kind regards
 Heinrich.

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Re: [R] Is R-2.10.0 released already

2009-12-02 Thread Duncan Murdoch


On 01/12/2009 9:19 PM, Hiroto Miyoshi wrote:

Dear R users, and Dr. Delagard

I got an R-announce message which tells that
R-2.10.0 will be released on December 4, 2009.


Could you post a copy of that message?  The message I saw said

This is to announce that we plan to release R version 2.10.1 on Monday,
December 14, 2009.

which has a couple of differences from what you describe.

Duncan Murdoch



Houever, it seems the R of that version was already
released. At leased I made sure that the R of that version
was in Cran and Univ. of Tsukuba, and also Univ. of Toronto.

And that version is quite odd because each package is in
a folder whih is named coffin. I am seriously worrying that
Cran site is hacked and someone might have placed a mallicious
version.

Please do take a look at the version and make sure if it is
really a valid version.

Sincerely

Hiroto




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and provide commented, minimal, self-contained, reproducible code.

Re: [R] R script From PHP


On 12/02/2009 10:43 AM, Amrit Nandan wrote:

I tried calling R from a shell script and it works. This is an example
file rscript.sh

R --no-save  EOT
x-2*pi
print(cbind(x,sin(x)))
quit(no)
EOT

This works perfectly on the Linux machine in which I have logged in via
SSH using the command (./rscript.sh)

I tried running this command using php

html
?php

$output = array();
$$retval = 0;
$a = shell_exec('./rscript.sh'. 21);
//print phpinfo();
print $a;

?
/html

this does not work and gives me this error:

./rscript.sh: line 1: R: command not found


Maybe shell_exec('sh ./rscript.sh 21' ) instead, maybe you need to 
have the full path of R.


With this design, you are going to start a new R session each time you 
want anything to be computed, and you are going to have to format the 
result of the R code as a string and parse this string back in php.




You really should look into Rserve and its new php client, which I think 
will solve all of these problems at once.


Just download the version 0.6-1 from here : 
http://www.rforge.net/Rserve/files/


$ wget http://www.rforge.net/src/contrib/Rserve_0.6-1.tar.gz
# R CMD INSTALL Rserve_0.6-1.tar.gz

start the server

$ R CMD Rserve

grab the php client, and include it into your php application

$ tar zxvf Rserve_0.6-1.tar.gz
$ less Rserve/src/client/php/simple.php

If you try this route, be aware that the php client is very new. also 
you probably want to post questions regarding it on this mailing list :

http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel

Romain



Anybody familiar with this?

On Tue, Dec 1, 2009 at 5:35 PM, Romain Francois
romain.franc...@dbmail.com mailto:romain.franc...@dbmail.com wrote:

On 12/01/2009 12:48 PM, Hrishi Mittal wrote:

Hi Amrit,

I believe you can you use the PHP system command to call Rscript
or R CMD. I
don't know much PHP but this page might be useful -
http://php.net/manual/en/function.system.php.

You might also want to look at rapache -
http://biostat.mc.vanderbilt.edu/rapache/

Good luck with your project and do post a link to your webpage
when you get
it running.


There is also a simple php client to Rserve in the next version of
Rserve. http://www.rforge.net/Rserve/index.html


--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/FtUu : new package : highlight
|- http://tr.im/EAD5 : LondonR slides
`- http://tr.im/BcPw : celebrating R commit #5

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Re: [R] Is R-2.10.0 released already

2009-12-02 Thread Peter Dalgaard

Duncan Murdoch wrote:
 On 01/12/2009 9:19 PM, Hiroto Miyoshi wrote:
 Dear R users, and Dr. Delagard

 I got an R-announce message which tells that
 R-2.10.0 will be released on December 4, 2009.
 
 Could you post a copy of that message?  The message I saw said
 
 This is to announce that we plan to release R version 2.10.1 on Monday,
 December 14, 2009.
 
 which has a couple of differences from what you describe.


There's an informal tradition that those announcements contain at least
one mistake, but apparently I forgot this time, so users have to make up
their own

-pd



-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk)  FAX: (+45) 35327907

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[R] Joint density kde2d works improperly?

2009-12-02 Thread Trafim

Dear all,

Please, look at the following code:

attach(geyser)
f1 - kde2d(duration, waiting, n = 5)

a - 0
for (i in 1:5){
 for (j in 1:5){
 a - a + f1$z[i,j]
 }
}

As far as I understood from Help kde2d returns matrix elements of which are
values of joint probability mass function Pr(X=x,Y=y) therefore, sum of its
elements should sum to 1.
Which is not the case from my check.
Where is the problem here?

Thanks a lot.

[[alternative HTML version deleted]]

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Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread Duncan Murdoch


On 01/12/2009 9:48 PM, Charlotte Maia wrote:

Hi,

When I reply to a post, it generally appears as a separate thread,
rather than branching off the original post.

Anyone know what I'm doing wrong?


Individual messages have a Message-ID header; for example, your 
message has this one:


Message-ID: b7bfe54e0912011848n130c22a6g8d7da8c4ca505...@mail.gmail.com

Your mail client (or the archive one) performs threading based on clues 
in the header, including ones like


References: 4b15931602cb00056...@medicine.umaryland.edu
4b15931702cb00056...@medicine.umaryland.edu
4b15931702cb00056...@medicine.umaryland.edu

and

In-Reply-To: 4b15931702cb00056...@medicine.umaryland.edu

(from a different message).  Your problem is that because you are using 
the digest, you aren't inserting those headers (or perhaps yours refer 
to the digest, not the individual message), so the clients don't realize 
your messages are replies.


There may be ways to trigger the threading without knowing the message 
ID, because sometimes message IDs in References are not right.  For 
example, the References list that I posted was from John Sorkin's reply 
to you, which my client correctly threaded even though it refers to a 
different message ID than yours (presumably something local to his system).


Duncan Murdoch




Noting I am currently receiving a couple of the lists in digest form.


kind regards


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Re: [R] R script From PHP

RServe looks exciting but the problem is that I am not sure whether I would
be allowed to install anything on the linux server on which I am working.

On Wed, Dec 2, 2009 at 3:40 PM, Romain Francois
romain.franc...@dbmail.comwrote:

 On 12/02/2009 10:43 AM, Amrit Nandan wrote:

 I tried calling R from a shell script and it works. This is an example
 file rscript.sh

 R --no-save  EOT
 x-2*pi
 print(cbind(x,sin(x)))
 quit(no)
 EOT

 This works perfectly on the Linux machine in which I have logged in via
 SSH using the command (./rscript.sh)

 I tried running this command using php

 html
 ?php

 $output = array();
 $$retval = 0;
 $a = shell_exec('./rscript.sh'. 21);
 //print phpinfo();
 print $a;

 ?
 /html

 this does not work and gives me this error:

 ./rscript.sh: line 1: R: command not found


 Maybe shell_exec('sh ./rscript.sh 21' ) instead, maybe you need to have
 the full path of R.

 With this design, you are going to start a new R session each time you want
 anything to be computed, and you are going to have to format the result of
 the R code as a string and parse this string back in php.



 You really should look into Rserve and its new php client, which I think
 will solve all of these problems at once.

 Just download the version 0.6-1 from here :
 http://www.rforge.net/Rserve/files/

 $ wget http://www.rforge.net/src/contrib/Rserve_0.6-1.tar.gz
 # R CMD INSTALL Rserve_0.6-1.tar.gz

 start the server

 $ R CMD Rserve

 grab the php client, and include it into your php application

 $ tar zxvf Rserve_0.6-1.tar.gz
 $ less Rserve/src/client/php/simple.php

 If you try this route, be aware that the php client is very new. also you
 probably want to post questions regarding it on this mailing list :
 http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel

 Romain


  Anybody familiar with this?

 On Tue, Dec 1, 2009 at 5:35 PM, Romain Francois
 romain.franc...@dbmail.com mailto:romain.franc...@dbmail.com wrote:

On 12/01/2009 12:48 PM, Hrishi Mittal wrote:

Hi Amrit,

I believe you can you use the PHP system command to call Rscript
or R CMD. I
don't know much PHP but this page might be useful -
http://php.net/manual/en/function.system.php.

You might also want to look at rapache -
http://biostat.mc.vanderbilt.edu/rapache/

Good luck with your project and do post a link to your webpage
when you get
it running.


There is also a simple php client to Rserve in the next version of
Rserve. http://www.rforge.net/Rserve/index.html


 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
 `- http://tr.im/BcPw : celebrating R commit #5



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R script From PHP

Also I tried out your method, it returns the same error. Another thing, If I
change the top line in rscript.sh to R --slave it just gives me a neat
output. I am not sure why running the shell script directly from within the
same folder is working where as from php it is not recognising R command.

On Wed, Dec 2, 2009 at 3:47 PM, Amrit Nandan amrit.nan...@gmail.com wrote:

 RServe looks exciting but the problem is that I am not sure whether I would
 be allowed to install anything on the linux server on which I am working.


 On Wed, Dec 2, 2009 at 3:40 PM, Romain Francois 
 romain.franc...@dbmail.com wrote:

 On 12/02/2009 10:43 AM, Amrit Nandan wrote:

 I tried calling R from a shell script and it works. This is an example
 file rscript.sh

 R --no-save  EOT
 x-2*pi
 print(cbind(x,sin(x)))
 quit(no)
 EOT

 This works perfectly on the Linux machine in which I have logged in via
 SSH using the command (./rscript.sh)

 I tried running this command using php

 html
 ?php

 $output = array();
 $$retval = 0;
 $a = shell_exec('./rscript.sh'. 21);
 //print phpinfo();
 print $a;

 ?
 /html

 this does not work and gives me this error:

 ./rscript.sh: line 1: R: command not found


 Maybe shell_exec('sh ./rscript.sh 21' ) instead, maybe you need to have
 the full path of R.

 With this design, you are going to start a new R session each time you
 want anything to be computed, and you are going to have to format the result
 of the R code as a string and parse this string back in php.



 You really should look into Rserve and its new php client, which I think
 will solve all of these problems at once.

 Just download the version 0.6-1 from here :
 http://www.rforge.net/Rserve/files/

 $ wget http://www.rforge.net/src/contrib/Rserve_0.6-1.tar.gz
 # R CMD INSTALL Rserve_0.6-1.tar.gz

 start the server

 $ R CMD Rserve

 grab the php client, and include it into your php application

 $ tar zxvf Rserve_0.6-1.tar.gz
 $ less Rserve/src/client/php/simple.php

 If you try this route, be aware that the php client is very new. also you
 probably want to post questions regarding it on this mailing list :
 http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel

 Romain


  Anybody familiar with this?

 On Tue, Dec 1, 2009 at 5:35 PM, Romain Francois
 romain.franc...@dbmail.com mailto:romain.franc...@dbmail.com wrote:

On 12/01/2009 12:48 PM, Hrishi Mittal wrote:

Hi Amrit,

I believe you can you use the PHP system command to call Rscript
or R CMD. I
don't know much PHP but this page might be useful -
http://php.net/manual/en/function.system.php.

You might also want to look at rapache -
http://biostat.mc.vanderbilt.edu/rapache/

Good luck with your project and do post a link to your webpage
when you get
it running.


There is also a simple php client to Rserve in the next version of
Rserve. http://www.rforge.net/Rserve/index.html


 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
 `- http://tr.im/BcPw : celebrating R commit #5




[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread Peter Dalgaard

Charlotte Maia wrote:
 On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:
 I don't know what you are doing wrong because I don't know exactly what you 
 are doing. I do know that I don't have your problem when I simply reply to a 
 message without touching the subject line.
 John
 
 Could you clarify the notion of simply reply.
 There is no obvious reply links in either the archive page, or the digest.
 
 In the case, where someone sends me an email, such have you have done,
 I can simply reply.
 
 However, in general this option is not available.
 

Things look normal from here; e.g., the above is threaded as a child of
Sorkin's mail, and it has the appropriate

In-Reply-To: 4b15931702cb00056...@medicine.umaryland.edu

header.

I.e., I suspect that your own mail client may be doing you in. (Some
mail clients, like Thunderbird, will even thread on the text of the
Subject field,  which can be a bit of a pain when people choose
unoriginal subjects like Question.)

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk)  FAX: (+45) 35327907

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Calling R (GNU R) functions from Common Lisp, how?

2009-12-02 Thread TJW

Hi Lisp users,

I'm a user of both Common Lisp and R (GNU R).
I found R has a rich collection of statistical and numerical
computation functions, while it is not as extensible as Lisp (Common
Lisp).
I considered Lisp-Stat but its only implementation is not in the
usuall Common Lisp, and the available functions in CRAN are far richer
than Lisp-Stat currently has.

I want to know if there is already an existing way of calling R
functions from within Common Lisp?
If no, please point me to relevant resources so that I can create one
(that works in a platform-independent manner).

Best,
tjw

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R script From PHP

Some more development: I found the directory of R in the Root

It is
/usr/bin/R

I did a ls -l R and got this output
-rwxr-xr-x 1 root root 6642 Jan  9  2006 R (This looks like in CHMOD 755
already)

So I modified my shell script

#!/bin/sh
cd /usr/bin/
pwd
R --slave EOF
x-2*pi
print(cbind(x,sin(x)))
quit(no)
EOF

This is returning me the same error when I try to execute it via my PHP
shell_exec('./rscript.sh'. 21);

Error:
/usr/bin ./rscript.sh: line 4: R: command not found

This is really wierd.

On Wed, Dec 2, 2009 at 3:52 PM, Amrit Nandan amrit.nan...@gmail.com wrote:

 Also I tried out your method, it returns the same error. Another thing, If
 I change the top line in rscript.sh to R --slave it just gives me a neat
 output. I am not sure why running the shell script directly from within the
 same folder is working where as from php it is not recognising R command.


 On Wed, Dec 2, 2009 at 3:47 PM, Amrit Nandan amrit.nan...@gmail.comwrote:

 RServe looks exciting but the problem is that I am not sure whether I
 would be allowed to install anything on the linux server on which I am
 working.


 On Wed, Dec 2, 2009 at 3:40 PM, Romain Francois 
 romain.franc...@dbmail.com wrote:

 On 12/02/2009 10:43 AM, Amrit Nandan wrote:

 I tried calling R from a shell script and it works. This is an example
 file rscript.sh

 R --no-save  EOT
 x-2*pi
 print(cbind(x,sin(x)))
 quit(no)
 EOT

 This works perfectly on the Linux machine in which I have logged in via
 SSH using the command (./rscript.sh)

 I tried running this command using php

 html
 ?php

 $output = array();
 $$retval = 0;
 $a = shell_exec('./rscript.sh'. 21);
 //print phpinfo();
 print $a;

 ?
 /html

 this does not work and gives me this error:

 ./rscript.sh: line 1: R: command not found


 Maybe shell_exec('sh ./rscript.sh 21' ) instead, maybe you need to have
 the full path of R.

 With this design, you are going to start a new R session each time you
 want anything to be computed, and you are going to have to format the result
 of the R code as a string and parse this string back in php.



 You really should look into Rserve and its new php client, which I think
 will solve all of these problems at once.

 Just download the version 0.6-1 from here :
 http://www.rforge.net/Rserve/files/

 $ wget http://www.rforge.net/src/contrib/Rserve_0.6-1.tar.gz
 # R CMD INSTALL Rserve_0.6-1.tar.gz

 start the server

 $ R CMD Rserve

 grab the php client, and include it into your php application

 $ tar zxvf Rserve_0.6-1.tar.gz
 $ less Rserve/src/client/php/simple.php

 If you try this route, be aware that the php client is very new. also you
 probably want to post questions regarding it on this mailing list :
 http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel

 Romain


  Anybody familiar with this?

 On Tue, Dec 1, 2009 at 5:35 PM, Romain Francois
 romain.franc...@dbmail.com mailto:romain.franc...@dbmail.com wrote:

On 12/01/2009 12:48 PM, Hrishi Mittal wrote:

Hi Amrit,

I believe you can you use the PHP system command to call Rscript
or R CMD. I
don't know much PHP but this page might be useful -
http://php.net/manual/en/function.system.php.

You might also want to look at rapache -
http://biostat.mc.vanderbilt.edu/rapache/

Good luck with your project and do post a link to your webpage
when you get
it running.


There is also a simple php client to Rserve in the next version of
Rserve. http://www.rforge.net/Rserve/index.html


 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
 `- http://tr.im/BcPw : celebrating R commit #5





[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R script From PHP

2009-12-02 Thread Hrishi Mittal


I agree with Romain that you should probably try and get Rserve to work as
that is a much better way. However, to get your commandline version working,
I suggest you use the Rscript comman instead of a bash script. So let's say
you save your R script as a myscript.R file. Then do:

shell_exec('Rscript /path/to/myscript.R'. 21);

If that still gives you an error like Rscript command not found, then you
need to make sure your R bin directory is added to the PATH system variable.
-- 
View this message in context: 
http://n4.nabble.com/R-script-From-PHP-tp931996p932992.html
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__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Calling R (GNU R) functions from Common Lisp, how?

2009-12-02 Thread Hrishi Mittal


RCL looks promising - http://common-lisp.net/project/rcl/

For quick and short calls to R, you can always use the system commands in CL
to call R CMD or Rscript.


tsunhin wong wrote:
 
 Hi Lisp users,
 
 I'm a user of both Common Lisp and R (GNU R).
 I found R has a rich collection of statistical and numerical
 computation functions, while it is not as extensible as Lisp (Common
 Lisp).
 I considered Lisp-Stat but its only implementation is not in the
 usuall Common Lisp, and the available functions in CRAN are far richer
 than Lisp-Stat currently has.
 
 I want to know if there is already an existing way of calling R
 functions from within Common Lisp?
 If no, please point me to relevant resources so that I can create one
 (that works in a platform-independent manner).
 
 Best,
 tjw
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 

-- 
View this message in context: 
http://n4.nabble.com/Calling-R-GNU-R-functions-from-Common-Lisp-how-tp932953p932994.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] R Batch Mode Customized Input

2009-12-02 Thread koj


Dear all, 

I use R in Batch Mode with the following syntax:

X:\...\Rcmd BATCH --slave X\...\test.R X:\...\Log.txt 

It works very fine. 

Now I want to write a function and customize the input for my R-File, e.g I
want to define the start and the end date.

Let's assume that test.R includes only a function like this: 

analysis-function(start.date,end.date){...}

Is it possible to give the arguments of the function via Batch Mode, e.g.
start.date=c(2009-10-01) and end.date=c(2009-10-31)? Normally I would do
this as following: result-analysis(c(2009-10-01),c(2009-10-31)). 

Going away from the function: It were sufficent, if the R-Script test.R were
running and recognizing start.date and end.date in the same manner as I
would write the dates in the top of the file.

The background: I am searching for a possibility, that my colleagues can use
my files without programming skills in R and without the necessity of
opening R. The batch mode is a great thing at this point - the actual
problem for me is the missing  possibility of define some details.

Have you any suggestions to solve my problem? Probably there are other
possibilities I don't see at the moment. If other people could enter the
dates in the example (in which way respectively in which platform is to
define) and start the R-File without R-knowledge, in whatever way, this were
the optimal solution. 

Thank you very much in advance,

Jens.













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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] pictures_in_a_matrix

2009-12-02 Thread Claudia Hantschel


Dear all,
how is it possible to upload first two figures (original: jpeg files, 
these are two pictures from a micrope) in a layout(matrix(c(1,2,3), 
1,3), widths=c(2.5,1.5, 2.5), heights=c(1,1) ) (the last field of the 
matrix is for a barplot)? The hole matrix is then need to be safed as 
eps-format. Does it make sense to upload these figures in R?

Many thanks for any help! Claudia.

--
*
Dr. Claudia Hantschel
Züchtungsbiologie und Molekulare Genetik
Department für Nutzpflanzen- und Tierwissenschaften
Humboldt-Universität zu Berlin
Invalidenstraße 42
10115 Berlin

Breeding Biology and Molecular Genetics
Department for Crop and Animal Sciences
Humboldt-University of Berlin
Invalidenstraße 42
10115 Berlin
Germany

phone: 0049 30 2093 6304
fax:   0049 30 2093 6397

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread Tony B

To be honest, I've never figured this out either. However, if you're
familiar with the gmail way of threading emails, just bookmark and use
google groups:

http://groups.google.co.uk/group/r-help-archive

It's the easiest way I've personally found, and has a very intuitive
interface.

HTH,
Tony Breyal



On 2 Dec, 03:42, Charlotte Maia mai...@gmail.com wrote:
 On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:

  I don't know what you are doing wrong because I don't know exactly what you 
  are doing. I do know that I don't have your problem when I simply reply to 
  a message without touching the subject line.
  John

 Could you clarify the notion of simply reply.
 There is no obvious reply links in either the archive page, or the digest.

 In the case, where someone sends me an email, such have you have done,
 I can simply reply.

 However, in general this option is not available.

 --
 Charlotte Maiahttp://sites.google.com/site/maiagx/home

 __
 r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Histogram probabilities 1 ????!!!

2009-12-02 Thread Trafim

Hi everybody,

well, I definitely don't understand anything.
Why the hist function with freq=FALSE gives such a strange result???

R - c(-1.10,  0.79, -1.17, -0.53, -0.26, -0.22,  0.29, -0.26, -0.26,  0.39)
hist(R, freq=FALSE, breaks=10)

Thanks everybody

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread Hrishi Mittal


I use Nabble which it has a reply button and seems to work fine. The old
version was very slow but the new one is fast.



Peter Dalgaard wrote:
 
 Charlotte Maia wrote:
 On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:
 I don't know what you are doing wrong because I don't know exactly what
 you are doing. I do know that I don't have your problem when I simply
 reply to a message without touching the subject line.
 John
 
 Could you clarify the notion of simply reply.
 There is no obvious reply links in either the archive page, or the
 digest.
 
 In the case, where someone sends me an email, such have you have done,
 I can simply reply.
 
 However, in general this option is not available.
 
 
 Things look normal from here; e.g., the above is threaded as a child of
 Sorkin's mail, and it has the appropriate
 
 In-Reply-To: 4b15931702cb00056...@medicine.umaryland.edu
 
 header.
 
 I.e., I suspect that your own mail client may be doing you in. (Some
 mail clients, like Thunderbird, will even thread on the text of the
 Subject field,  which can be a bit of a pain when people choose
 unoriginal subjects like Question.)
 
 -- 
O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
  (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
 ~~ - (p.dalga...@biostat.ku.dk)  FAX: (+45) 35327907
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 

-- 
View this message in context: 
http://n4.nabble.com/Replying-to-Posts-Within-Same-Thread-tp932713p932995.html
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Histogram probabilities 1 ????!!!

2009-12-02 Thread Peter Flom

Trafim rdapam...@gmail.com wrote


well, I definitely don't understand anything.
Why the hist function with freq=FALSE gives such a strange result???

R - c(-1.10,  0.79, -1.17, -0.53, -0.26, -0.22,  0.29, -0.26, -0.26,  0.39)
hist(R, freq=FALSE, breaks=10)



The total AREA has to equal 1, which does not mean that the highest height has 
to be less than 1.

It looks like each of your bars is about .2 wide; area = height*width, so  
that high one in the middle has area of about 2*.2 = .4

HTH

Peter

Peter L. Flom, PhD
Statistical Consultant
Website: www DOT peterflomconsulting DOT com
Writing; http://www.associatedcontent.com/user/582880/peter_flom.html
Twitter:   @peterflom

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread John Sorkin

I hit the reply all button on my Email client if I want the message to go both 
to the person who wrote the Email and the R listserver.
John




John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 
Charlotte Maia mai...@gmail.com 12/1/2009 10:42 PM 
On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:
 I don't know what you are doing wrong because I don't know exactly what you 
 are doing. I do know that I don't have your problem when I simply reply to a 
 message without touching the subject line.
 John

Could you clarify the notion of simply reply.
There is no obvious reply links in either the archive page, or the digest.

In the case, where someone sends me an email, such have you have done,
I can simply reply.

However, in general this option is not available.

-- 
Charlotte Maia
http://sites.google.com/site/maiagx/home 

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help 
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 
and provide commented, minimal, self-contained, reproducible code.

Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Histogram probabilities 1 ????!!!

Y-axis in your code is ``Counts'' irrelevant to probabilities.

Guo-Hao Huang

--
From: Trafim rdapam...@gmail.com
Sent: Wednesday, December 02, 2009 7:35 PM
To: r-help@r-project.org
Subject: [R] Histogram probabilities 1 !!!

Hi everybody,

well, I definitely don't understand anything.
Why the hist function with freq=FALSE gives such a strange result???

R - c(-1.10,  0.79, -1.17, -0.53, -0.26, -0.22,  0.29, -0.26, -0.26,  0.39)
hist(R, freq=FALSE, breaks=10)

Thanks everybody

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Normal tests disagree?

2009-12-02 Thread Ted Harding

On 01-Dec-09 23:11:20, rkevinbur...@charter.net wrote:
 If I have data that I feed into shapio.test and jarque.bera.test yet
 they seem to disagree. What do I use for a decision?
 
 For my data set I have p.value of 0.05496421 returned from the
 shapiro.test and 0.882027 returned from the jarque.bera.test. I have
 included the data set below.
 
 Thank you.
 
 Kevin
[Data snipped]

The reason is that the Jarque-Bera test (JB) works with the squared
skewness plus 1/4 of (kurtosis - 3)^2. For a Normal distribution,
the skewness is zero and the kurtosis is 3. Hence large values of JB
are evidence against the hypothesis that the distribution is Normal,
in the basis that skewness and/or kurtosis depart from the values
to be expected for a Normal distribution.

However, it is perfectly possible to get skewness near 0, and kurtosis
near 3, for manifestly non-Normal distributions. I get Skewness=0.014
and Kurtosis=3.32 for your data, both quite close to the Normal values.

However, you only have to look at the histogram to see that the
distribution has a distinctly non-Normal appearance:

   hist(x,breaks=20)

The Shapiro-Wilk test, on the other hand, works (broadly speaking)
in terms of standardised spacings between the order statistics
of the sample, compared with what they should be from a Normal.
It is therefore sensitive to features of the sample which are rather
different to the features that the J-B test is sensitive to.

Given the appearance of the histogram, it is to be expected that
many of the spacings between order statistics are different from
what are to be expected from a Normal distribution.

Much of this, and also the insensitivity of the J-B test, arises
from the clump of values at the top of the range (6 out of the 59
between 1.83 and 2.00). Leave these out and you get quite different
results.

The following is an explicit implementation of the J-B test, based
on the Wikipedia description, and using the chi-squared(2) approximation
for the P-value (and also returning the skewness and kurtosis):

  jarque.bera - function(x){
m1 - mean(x); m2 - mean((x-m1)^2)
m3 - mean((x-m1)^3) ; m4 - mean((x-m1)^4)
n - length(x) ; S - m3/(m2^(3/2)) ; K - m4/(m2^2)
JB - (n/6)*(S^2 + ((K-3)^2)/4)
P - 1-pchisq(JB,2)
list(JB=JB,P=P,S=S,K=K)
  }

For your original data x (as explicitly extracted by Ben Bolker):

  jarque.bera(x)
  # $JB
  # [1] 0.251065
  # $P
  # [1] 0.882027  # (As you found yourself)
  # $S
  # [1] 0.01396711
  # $K
  # [1] 3.318352

For the data excluding the 6 values above 1.83:

  jarque.bera(x[x=1.83])
  # $JB
  # [1] 6.047885
  # $P
  # [1] 0.04860919
  # $S
  # [1] -0.6831185
  # $K
  # [1] 3.933842

So excluding these values has produced a distinct negative skewness
and a kurtosis distinctly greater than 3. Hence those 6 values were
primarily responsible for almost completely eliminating the skewness
and the kurtosis of the remainder of the distribution, and hence
frustrating the J-B test.

Now compare with the Shapiro-Wilk test:

  shapiro.test(x)
  # Shapiro-Wilk normality test
  # data:  x
  # W = 0.9608, p-value = 0.05496

so the S-W P-value 0.05496 for the full data is close to the
J-B P-value 0.04861 for the reduced data. Now compare with the
S-W test on the reduced data:

  shapiro.test(x[x = 1.83])
  # Shapiro-Wilk normality test
  # data:  x[x = 1.83] 
  # W = 0.9595, p-value = 0.06968

The S-W P-vale has increased slightly (from 0.055 to 0.070),
but the S-W test is still picking up the non-Normality in the
reduced dataset.

The summary is that the S-W test and the J-B test are looking
at different aspects of the data. The J-B test depends only on
two summary functions (skewness and kurtosis) as indices of
non-Normality, while the S-W test is sensitive to a wider
variation of the fine detail of the distribution of the data.

The failure of the J-B test to detect the non-Normality in the
data is primarily due to the fact that the 6 data values at the
top end have, in effect, compensated for the marked skewness
and kurtosis in the remainder of the data.

The ultimate lesson from all this is that different tests test
for different kinds of deperture from the Null Hypothesis.
See also Uwe Ligges's remarks ...

Ted.


E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 02-Dec-09   Time: 11:53:22
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[R] problems installing R packages

2009-12-02 Thread catuxa-2


Hi,
I´m trying to install new package in R (version 2.4.0) under windows vista
and i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
'C:/Program Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
It can´t open the file.
I check the compatibility with the version and is ok, I have no idea where's
the problem cause i'm the administrator and i've enough free space in the
hard disc.

Anyone could help me

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Re: [R] problems installing R packages

Could you install the latest R software in your computer?
In R-2.9.2, install.packages(mprobit) works well.

Guo-Hao Huang

--
From: catuxa-2 catuxa...@gmail.com
Sent: Wednesday, December 02, 2009 7:55 PM
To: r-help@r-project.org
Subject: [R]  problems installing R packages

Hi,
I´m trying to install new package in R (version 2.4.0) under windows vista
and i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
'C:/Program Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
It can´t open the file.
I check the compatibility with the version and is ok, I have no idea where's
the problem cause i'm the administrator and i've enough free space in the
hard disc.

Anyone could help me

-- 
View this message in context: 
http://n4.nabble.com/problems-installing-R-packages-tp933010p933010.html
Sent from the R help mailing list archive at Nabble.com.

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[R] category with respect to category

2009-12-02 Thread Ahmet Temiz


hello

 I have two categorical data and want to visualise them to see their changes?

 Which graph do you recommend me for category with respect to category ?

 kind regards

 
Ahmet Temiz
--
Open WebMail Project (http://openwebmail.org)


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Re: [R] explanation for left-side behaviour

2009-12-02 Thread Antje


Hi Don,

thanks for your answer. Okay, I should have mentioned the error messages 
I get for case 1 and 2 - sorry.
I was just surprised because the following does not give an error 
(though I feed with the factor vector):


substr(values,2,3)

[1] bc bc bc cd cd cd de de de

Obviously, the factor vector is converted to character somewhere, no?
I get the same result when typing:

substr(as.character(values),2,3)

So, the restriction that substr cannot take anything else than a 
character vector seems to be only in case I want to use the replace 
functionality instead of just extracting a substring. At least, that is 
my guess..


Ciao,
Antje




Don MacQueen wrote:

Read the help page for substr().
It says that the first argument should be a character vector.
The only one that works is the one where you gave it a character vector.

You said only third one works. But you didn't explain what you mean 
by works. It's always a good idea on r-help to show both what you 
expected, and what you actually got, so that people can understand 
exactly what the question is.


To explain a little further, let me number your three approaches.

[1]  substr(values,2,3) - ..

[2] substr(as.character(values),2,3) - ..

values - as.character(values)
[3] substr(values,2,3) - ..

With regard to case [1]
It makes no sense to replace character substrings in a factor. factors 
are really numbers, not characters. It's just that they have 
additional attributes that make them (sometimes) print as if the were 
characters. But they're not. And the error message (that you didn't 
report) says exactly that.


With regard to case [2]:
values and as.character(values) are not the same thing.
Therefore, replacing substrings in as.character(values) is not the 
same as replacing substrings in values. In this case, I would 
interpret the error message to indicate that R is trying to replace 
characters in a function. That makes sense, because you supplied a 
function, namely, as.character().


Case [3] works because you supplied a character vector.

-Don

At 9:57 AM +0100 12/1/09, Antje wrote:

Hi there,

I'm pretty sure that it's written down somewhere but I cannot find it 
so far.


The little example shows different approaches to replace a substring. 
Only the last one works. I think it has something to do with the fact 
that substr is used on the left side. Can anybody refer to an 
explanation for this behaviour?


Thanks a lot in advance!

Antje



values - factor(c(rep(abc,3), rep(bcd,3), rep(cde,3)))

substr(values,2,3) - ..
substr(as.character(values),2,3) - ..

values - as.character(values)
substr(values,2,3) - ..

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Re: [R] problems installing R packages


On 12/02/2009 12:55 PM, catuxa-2 wrote:


Hi,
I´m trying to install new package in R (version 2.4.0) under windows vista
and i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
'C:/Program Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
It can´t open the file.
I check the compatibility with the version and is ok, I have no idea where's
the problem cause i'm the administrator and i've enough free space in the
hard disc.

Anyone could help me


Try to time travel back in late 2006 when 2.4.0 was current, or upgrade 
to the current version of R (2.10.0) for which you might get support ... 
whichever way is easiest for you.


When you are done, please lend us your time travel machine so that we 
can get R 3.0.0 from the future.


Romain

--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/FtUu : new package : highlight
|- http://tr.im/EAD5 : LondonR slides
`- http://tr.im/BcPw : celebrating R commit #5

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[R] Cryptic error message from rfe (in caret package)

2009-12-02 Thread Richard R. Liu


When using the function rfe I receive the warning

In x == y : longer object length is not a multiple of shorter object  
length


more than 50 times.

I call rfe as follows:

nbProfile - rfe(features.train.50pct, truth.train.50pct, sizes =  
no.features, rfeControl = nbCtrl)


where
features.train.50pct	data frame of 8 named columns, each of 487 rows,  
numeric

truth.train.50pct   factor of 487 logical elements
sizes   1, 2, ..., 8
nbCtrl			rfeControl(functions = nbFuncs, method = cv, verbose = F,  
returnResamp = final)


Does anybody know to which objects the warnings refer?

Richard R. Liu
Dittingerstr. 33
CH-4053 Basel
Switzerland

Tel.:  +41 61 331 10 47
Mobil: +41 79 708 67 66
Email:  richard@pueo-owl.ch



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Re: [R] R script From PHP


On 12/02/2009 12:30 PM, Hrishi Mittal wrote:



I agree with Romain that you should probably try and get Rserve to work as
that is a much better way. However, to get your commandline version working,
I suggest you use the Rscript comman instead of a bash script. So let's say
you save your R script as a myscript.R file. Then do:

shell_exec('Rscript /path/to/myscript.R'. 21);

If that still gives you an error like Rscript command not found, then you
need to make sure your R bin directory is added to the PATH system variable.


... maybe shell_exec('/usr/bin/Rscript /path/to/myscript.R'. 21);

--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/FtUu : new package : highlight
|- http://tr.im/EAD5 : LondonR slides
`- http://tr.im/BcPw : celebrating R commit #5

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Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread Ted Harding

There is an issue which does not seem to have been raised yet in
this thread. In her original post, Charlotte Maia said she was
receiving messages in Digest form.

There are two Digest options: Get MIME or Plain Text Digests?
You can choose which one to use, if you opt for Digest format,
when setting your subscription options in the R-help configuration
page at

  https://stat.ethz.ch/mailman/options/r-help

In a plain-text Digest, all the messages are bundled into a single
message. Therefore when you reply to one of these you have to edit
out everything except the bit you are replying to; and also the
Thread-relevant headers of the original messages will heve been
suppressed -- only headers for the Dugest message will be present,
and these will have nothing to do with the threads that the separate
original messages belonged to.

On the other hand, in a MIME Digest, each of the original messages
is attached as a separate attachment, along with its original headers.
A mail agent which is MIME-Digest-aware will allow the user to
open up each attachment separately, as a single message, and reply
to that. Then the mail agent *should* incorporate these headers,
including those which identify the thread.

So, if you use Digest format, choose MIME Digest, and use a mail
agent which works properly!

Ted.

On 02-Dec-09 11:51:32, John Sorkin wrote:
 I hit the reply all button on my Email client if I want the message
 to go both to the person who wrote the Email and the R listserver.
 John
 
 John David Sorkin M.D., Ph.D.
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
 Charlotte Maia mai...@gmail.com 12/1/2009 10:42 PM 
 On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:
 I don't know what you are doing wrong because I don't know exactly
 what you are doing. I do know that I don't have your problem when I
 simply reply to a message without touching the subject line.
 John
 
 Could you clarify the notion of simply reply.
 There is no obvious reply links in either the archive page, or the
 digest.
 
 In the case, where someone sends me an email, such have you have done,
 I can simply reply.
 
 However, in general this option is not available.
 
 -- 
 Charlotte Maia
 http://sites.google.com/site/maiagx/home 


E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 02-Dec-09   Time: 12:15:01
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Re: [R] problems installing R packages

2009-12-02 Thread catuxa-2


Thank you!!!
It was just the run as administrator, sorry
But anyway, i canÂ´t change the version because i'm developing a java
aplication integraed with R, and the people who configurate te computer
recomended me not to change the  version. I'm not in love with late
2006!
But i think that i need to risk changing it, becaus i'm having lots of
problems
Do you know something of integrate eclipse and R???
Thank you



2009/12/2 Romain Francois [via R]
ml-node+933022-1560375...@n4.nabble.comml-node%2b933022-1560375...@n4.nabble.com


 On 12/02/2009 12:55 PM, catuxa-2 wrote:

 
  Hi,
  IÂ´m trying to install new package in R (version 2.4.0) under windows
 vista
  and i have problems. I always receive the same message:
  Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
  'C:/Program
 Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
  It canÂ´t open the file.
  I check the compatibility with the version and is ok, I have no idea
 where's
  the problem cause i'm the administrator and i've enough free space in the

  hard disc.
 
  Anyone could help me

 Try to time travel back in late 2006 when 2.4.0 was current, or upgrade
 to the current version of R (2.10.0) for which you might get support ...
 whichever way is easiest for you.

 When you are done, please lend us your time travel machine so that we
 can get R 3.0.0 from the future.

 Romain

 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
 `- http://tr.im/BcPw : celebrating R commit #5

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Re: [R] problems installing R packages

2009-12-02 Thread ONKELINX, Thierry

R 2.4.0 is obsolete. First update to the latest version (2.10.0, 2.10.1 will be 
available soon). And then try to install the packages.



ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie  Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics  Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than 
asking him to perform a post-mortem examination: he may be able to say what the 
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure 
that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens 
catuxa-2
Verzonden: woensdag 2 december 2009 12:55
Aan: r-help@r-project.org
Onderwerp: [R] problems installing R packages


Hi,
I´m trying to install new package in R (version 2.4.0) under windows vista and 
i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo 'C:/Program 
Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
It can´t open the file.
I check the compatibility with the version and is ok, I have no idea where's 
the problem cause i'm the administrator and i've enough free space in the hard 
disc.

Anyone could help me

--
View this message in context: 
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Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
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Re: [R] problems installing R packages

I think your keyboard has a punctuation problem. What's with all the 
exclamation points.


On 12/02/2009 01:18 PM, catuxa-2 wrote:


Thank you!!!
It was just the run as administrator, sorry
But anyway, i canÂ´t change the version because i'm developing a java
aplication integraed with R, and the people who configurate te computer
recomended me not to change the  version.


Then ask them for support.


I'm not in love with late
2006!
But i think that i need to risk changing it, becaus i'm having lots of
problems
Do you know something of integrate eclipse and R???


What do you mean ?


Thank you



2009/12/2 Romain Francois [via R]
ml-node+933022-1560375...@n4.nabble.comml-node%2b933022-1560375...@n4.nabble.com





On 12/02/2009 12:55 PM, catuxa-2 wrote:



Hi,
IÂ´m trying to install new package in R (version 2.4.0) under windows

vista

and i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
'C:/Program

Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'

It canÂ´t open the file.
I check the compatibility with the version and is ok, I have no idea

where's

the problem cause i'm the administrator and i've enough free space in the



hard disc.

Anyone could help me


Try to time travel back in late 2006 when 2.4.0 was current, or upgrade
to the current version of R (2.10.0) for which you might get support ...
whichever way is easiest for you.

When you are done, please lend us your time travel machine so that we
can get R 3.0.0 from the future.

Romain



--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/FtUu : new package : highlight
|- http://tr.im/EAD5 : LondonR slides
`- http://tr.im/BcPw : celebrating R commit #5

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[R] polygon graph

2009-12-02 Thread Jose Narillos de Santos

Hi all,

I have a matrix dd with dates and data. i WANT to create a grpah with shade
between the line and the zero axis. I´m trying to use polygon but something
doesn´ t work

Imagine.

I want to plot

g-read.table(dd.txt, col.names=c(fecha,DP))

g$fecha - as.Date(g$fecha, format=%d/%m/%Y)

t-g$fecha
st-length(g$DP)

ft-plot(t,g$DP,type=l,ylab=DP)

polygon(c(1, 1:st, st), c(0, g$USGDP, 0), col = blue)

abline(h = 0, lwd = 1, col = black)

If I ommit ploygon line the doc works properly (it plots a graph line).

But I want to colur the area below or over the line and the zero axis.

Can you guide or indicate because in this case polygon doesn´t work.

I attach the two files.



Thanks in advance for all.
31/03/1948  12.9
30/06/1948  24.9
30/09/1948  45.6
31/12/1948  24.2
31/03/1949  21.1
30/06/1949  -21.1
30/09/1949  -20.5
31/12/1949  -21.6
31/03/1950  23.8
30/06/1950  27.4
30/09/1950  10.4
31/12/1950  13.4
31/03/1951  10.3
30/06/1951  28.9
30/09/1951  26.8
31/12/1951  25.2
31/03/1952  24.9
30/06/1952  23.3
30/09/1952  22
31/12/1952  25.2
31/03/1953  26.1
30/06/1953  26.7
30/09/1953  25.4
31/12/1953  0.4
31/03/1954  -21.9
30/06/1954  -22.5
30/09/1954  -02.8
31/12/1954  22.8
g-read.table(PIB.txt, col.names=c(fecha,DP), sep=;,dec=,)

g$fecha - as.Date(g$fecha, format=%d/%m/%Y)

t-g$fecha
st-length(g$DP)

ft-plot(t,g$DP,type=l,ylab=US GDP, xlab=Tiempo,main=Evolución Histórica 
PIB US) 

#polygon(c(1, 1:st, st), c(0, g$DP, 0), col = blue)

grid()

abline(h = 0, lwd = 1, col = black)

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Re: [R] Incorporating the results of White's HCCM into a linear regression:

2009-12-02 Thread Frank E Harrell Jr


Yoseph,

What do you mean by 'incorporate into'?  If you mean to update the fit 
object's variance-covariance matrix, one approach might be


require(rms)
ols1 - ols(uer92 ~ ..., x=TRUE, y=TRUE)
ols1 - robcov(ols1)
anova(ols1); summary(ols1); ...  # uses 'robust' variancescovariances

You can substitute bootcov for robcov to use bootstrap estimates rather 
than Huber-White sandwich estimates.  Note that coefficients are unchanged.


Please provide your affiliation in e-mail postings.

Frank


Yoseph Zuback wrote:

Using hccm() I got a heteroscedasticity correction factor on the diagonal of
the return matrix, but I don't know how to incorporate this into my linear
model:

METHOD 1:


OLS1 - lm(formula=uer92~uer+low2+mlo+spec+degree+hit)


Coefficients:
  Estimate Std. Error t value Pr(|t|)
(Intercept) -0.0623377  0.0323461  -1.927 0.057217 .
uer  0.2274742  0.0758720   2.998 0.003541 **
low2 0.0276404  0.0375770   0.736 0.463973
mlo  0.1491490  0.0940637   1.586 0.116455
spec-0.1139978  0.0312223  -3.651 0.000445 ***
degree   0.0014694  0.0005316   2.764 0.006970 **
hit -0.0164365  0.0186028  -0.884 0.379376


hccm(OLS1)

  (Intercept)   uer  low2   mlo
spec
(Intercept)  9.057187e-04 -1.330377e-03 -3.486945e-05  2.184561e-04
-4.061445e-04
uer -1.330377e-03  5.471543e-03  3.513046e-04 -4.294427e-04
1.629196e-03
low2-3.486945e-05  3.513046e-04  1.378587e-03  1.241245e-04
-5.026434e-05
mlo  2.184561e-04 -4.294427e-04  1.241245e-04  9.796132e-03
-1.059611e-03
spec-4.061445e-04  1.629196e-03 -5.026434e-05 -1.059611e-03
9.777099e-04
degree   9.638288e-07 -2.907824e-05 -1.093692e-05 -1.867397e-05
-8.212461e-06
hit -3.299600e-04 -2.242984e-04  1.036364e-04 -8.158489e-04
3.994951e-05
   degree   hit
(Intercept)  9.638288e-07 -3.299600e-04
uer -2.907824e-05 -2.242984e-04
low2-1.093692e-05  1.036364e-04
mlo -1.867397e-05 -8.158489e-04
spec-8.212461e-06  3.994951e-05
degree   3.485174e-07  4.256330e-06
hit  4.256330e-06  4.154505e-04

I have reached my limit of R knowledge, any help is appreciated.

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Re: [R] problems installing R packages


The error messages indicated the ``zip.unpack'' problems.
Try to download the zip file to your HD, and reinstall the package again.
If this do not work, I hope that you can get a time machine.


 Guo-Hao Huang


--
From: catuxa-2 catuxa...@gmail.com
Sent: Wednesday, December 02, 2009 8:18 PM
To: r-help@r-project.org
Subject: Re: [R] problems installing R packages



Thank you!!!
It was just the run as administrator, sorry
But anyway, i canÂ´t change the version because i'm developing a java
aplication integraed with R, and the people who configurate te computer
recomended me not to change the  version. I'm not in love with late
2006!
But i think that i need to risk changing it, becaus i'm having lots of
problems
Do you know something of integrate eclipse and R???
Thank you



2009/12/2 Romain Francois [via R]
ml-node+933022-1560375...@n4.nabble.comml-node%2b933022-1560375...@n4.nabble.com





On 12/02/2009 12:55 PM, catuxa-2 wrote:


 Hi,
 IÂ´m trying to install new package in R (version 2.4.0) under windows
vista
 and i have problems. I always receive the same message:
 Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
 'C:/Program
Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
 It canÂ´t open the file.
 I check the compatibility with the version and is ok, I have no idea
where's
 the problem cause i'm the administrator and i've enough free space in 
 the


 hard disc.

 Anyone could help me

Try to time travel back in late 2006 when 2.4.0 was current, or upgrade
to the current version of R (2.10.0) for which you might get support ...
whichever way is easiest for you.

When you are done, please lend us your time travel machine so that we
can get R 3.0.0 from the future.

Romain

--
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Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/FtUu : new package : highlight
|- http://tr.im/EAD5 : LondonR slides
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Re: [R] Joint density kde2d works improperly?

2009-12-02 Thread Karl Ove Hufthammer

On Wed, 2 Dec 2009 11:14:14 +0100 Trafim rdapam...@gmail.com wrote:
 As far as I understood from Help kde2d returns matrix elements of which are
 values of joint probability mass function Pr(X=x,Y=y) therefore, sum of its
 elements should sum to 1.

No, they're values of a joint *density* function, which should usually 
*not* sum to 1.

-- 
Karl Ove Hufthammer

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Re: [R] Again on overlaying plots (a plot region within a plot region)



On Dec 2, 2009, at 3:15 AM, Ottorino-Luca Pantani wrote:


Dear R-users,
after seeking for help in R-search
I did not find any hint on my particular problem.
Countless help on true overlay, but nothing on this.


Please consider the following:

par(mfrow = c(2, 1))
T - seq(0, 20, by = 0.01)
## PLOT 1
plot(T,  30*exp(-0.65*T),
   type = l
   )
points(T, 30*exp(-0.26 * T), type = l, lty = F8)
points(T, 30*exp(-0.15 * T), type = l, lty = 39)
## PLOT 2
plot(T,  30*exp(-0.65*T),
   type = l,
   log= y
   )
points(T, 30*exp(-0.26 * T), type = l, lty = F8)
points(T, 30*exp(-0.15 * T), type = l, lty = 39)

What I would like to do is to draw a square plot of PLOT 1 and
then overlay the *entire* PLOT 2 on the upper right corner of PLOT 1,
when there's a lot of empty space
I have to do that because the publisher asked me not to waste
much space with figures.


The  subplot function in the excellent TeachingDemos package offer a  
complete solution.


http://finzi.psych.upenn.edu/R/library/TeachingDemos/html/subplot.html

--
David


I studied for some time the Paul Murrell's excellent book R  
Graphics,

but I did not find what I'm looking for.

As far as I understand, layout() is intended to flexibly
divide the plot region, not to subdivide the plot region
nor the figure region.

One solution could be to export PLOT 1 , say as png,
and then overlay on it PLOT 2 with pixmap() as in this example

http://www.stat.auckland.ac.nz/~paul/RGraphics/custombase-pixmap.R

but it seems to me a bit too much complicate

Thanks in advance for your time


--
Ottorino-Luca Pantani, Università di Firenze
Dip. Scienza del Suolo e Nutrizione della Pianta
P.zle Cascine 28 50144 Firenze Italia
Ubuntu 8.04.3 LTS -- GNU Emacs 23.0.60.1 (x86_64-pc-linux-gnu, GTK+  
Version 2.12.9)

ESS version 5.5 -- R 2.10.0

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[R] residuals from nls fit on time series

2009-12-02 Thread Jon Phillips

Hi,

I've been fitting some time-series data to 
x ~ c + m*t + a*exp(-t*k)
 with nls.  The fit works fine, and I can get the residuals out by
summary(fit)$residuals.  

My problem is that the residuals are not a time series, so when I plot
them, I get 0:1 on the x-axis, instead of eg. 0:0.5, or 0:5 (depends
on the exact fit).

Is there any way of getting the times out of the fit, or am I stuck?

Thanks

Jon Phillips


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Re: [R] A ggplot question

2009-12-02 Thread Megh


Hi all, I want be more clear what I want to do. Please consider following
code :

ggplot(diamonds, aes(carat, ..density..)) + geom_histogram(binwidth = 0.2,
aes(fill = cut)) + facet_grid(. ~ cut)

Here you see there is no need for the color-pallet named cut, as the
sub-plot headings take care of them. My question is how I can remove the
color-pallet. Your help will be highly appreciated.

Thanks,


Megh wrote:
 
 Thanks Ista for your mail. Here I wanted to have control on color-pallet.
 It is because, here my entire plot window is subdivided in 3 sub-plots
 horizontally, on basis if a factor-variable which contains three factors, 
 using facet_grid(). Each sub-plot contains scatter-plot. I want to color
 the points of each scatter-plot based on the corresponding factor
 (contained in factor-variable). Therefore as you might agree in this case,
 there is no need for additional color-pallet as the factor-description is
 handled by facet_grid() function itself.
 
 Any better idea how I can hide color-pallet?
 
 Thanks,
 
 
 
 Ista Zahn wrote:
 
 There was a recent discussion of the ggplot2 mailing list about a
 similar issue. The first question is how will people know what the
 colors mean if you remove the legend?
 
 -Ish
 
 On Tue, Dec 1, 2009 at 11:41 PM, Megh megh700...@yahoo.com wrote:

 Let consider following plot :

 p - ggplot(mtcars, aes(mpg, wt))
     p + geom_point(colour=grey50, size = 4) + geom_point(aes(colour =
 cyl))

 Now I want R to hide the color-pallet on cyl, placed in the right edge
 completely. Can anyone please guide me how to do that?

 Thanks,
 --
 View this message in context:
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 Sent from the R help mailing list archive at Nabble.com.

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 Department of Clinical and Social Psychology
 http://yourpsyche.org
 
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Re: [R] Joint density kde2d works improperly?

2009-12-02 Thread Trafim Vanishek

Dear Dennis, thanks a lot for your response.
I have two time series and need to approximate there joint density.

The only thing I cannot find out is how to find the values of this function
in the points not from the resulting grid matrix

Thanks a lot

You're using a function that provides an estimate of a *continuous*
 bivariate density
 to approximate a bivariate discrete distribution? If your joint
 distribution is discrete, there are
 better ways to visualize it, and I'll leave it up to you to discover how.
 (Hint: look at the 3D
 graphics packages.)

 DM

 On Wed, Dec 2, 2009 at 2:14 AM, Trafim rdapam...@gmail.com wrote:

 Dear all,

 Please, look at the following code:

 attach(geyser)
 f1 - kde2d(duration, waiting, n = 5)

 a - 0
 for (i in 1:5){
  for (j in 1:5){
  a - a + f1$z[i,j]
  }
 }

 As far as I understood from Help kde2d returns matrix elements of which
 are
 values of joint probability mass function Pr(X=x,Y=y) therefore, sum of
 its
 elements should sum to 1.
 Which is not the case from my check.
 Where is the problem here?

 Thanks a lot.

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Re: [R] Cryptic error message from rfe (in caret package)

2009-12-02 Thread Max Kuhn

Good etiquette would be to email the maintainer (me) with a
reproducibility example and the results of sessionInfo().

Max

On Wed, Dec 2, 2009 at 7:13 AM, Richard R. Liu richard@pueo-owl.ch wrote:
 When using the function rfe I receive the warning

 In x == y : longer object length is not a multiple of shorter object length

 more than 50 times.

 I call rfe as follows:

 nbProfile - rfe(features.train.50pct, truth.train.50pct, sizes =
 no.features, rfeControl = nbCtrl)

 where
 features.train.50pct    data frame of 8 named columns, each of 487 rows,
 numeric
 truth.train.50pct       factor of 487 logical elements
 sizes                   1, 2, ..., 8
 nbCtrl                  rfeControl(functions = nbFuncs, method = cv,
 verbose = F, returnResamp = final)

 Does anybody know to which objects the warnings refer?

 Richard R. Liu
 Dittingerstr. 33
 CH-4053 Basel
 Switzerland

 Tel.:  +41 61 331 10 47
 Mobil: +41 79 708 67 66
 Email:  richard@pueo-owl.ch




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Re: [R] Calling R (GNU R) functions from Common Lisp, how?



On Dec 2, 2009, at 6:34 AM, Hrishi Mittal wrote:



RCL looks promising - http://common-lisp.net/project/rcl/


It seems more than a bit worrisome that the above page currently ends  
with complex objects (in particular data frames) are handled very  
poorly. Dataframes may not be a fundamental data type, but they are  
arguably the dominant structure in typical R programmming.


For quick and short calls to R, you can always use the system  
commands in CL

to call R CMD or Rscript.


tsunhin wong wrote:


Hi Lisp users,

I'm a user of both Common Lisp and R (GNU R).
I found R has a rich collection of statistical and numerical
computation functions, while it is not as extensible as Lisp (Common
Lisp).
I considered Lisp-Stat but its only implementation is not in the
usuall Common Lisp, and the available functions in CRAN are far  
richer

than Lisp-Stat currently has.

I want to know if there is already an existing way of calling R
functions from within Common Lisp?
If no, please point me to relevant resources so that I can create one
(that works in a platform-independent manner).

Best,
tjw



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West Hartford, CT

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Re: [R] category with respect to category

2009-12-02 Thread Peter Ehlers


?mosaicplot

 -Peter Ehlers

Ahmet Temiz wrote:

hello

 I have two categorical data and want to visualise them to see their changes?

 Which graph do you recommend me for category with respect to category ?

 kind regards

 
Ahmet Temiz

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Re: [R] sort a data frame by a vector

2009-12-02 Thread Hao Cen

Thanks to all who replied. Issue solved

Jeff

On Wed, December 2, 2009 12:52 am, Don MacQueen wrote:
 This looks like a job for match().


 vec = c(C, A, B)

 dataDF = data.frame(A1 = c(B, A, C), A2 = c(1,2,3))


 dataDF[match(dataDF$A1,vec),]
 A1 A2
 3  C  3
 2  A  2
 1  B  1


 -Don



 At 10:36 PM -0500 12/1/09, Hao Cen wrote:

 Hi,




 I have a a vector  and a data frame with two columns


 vec = c(C, A, B)

 dataDF = data.frame(A1 = c(B, A, C), A2 = c(1,2,3))



 I would like to sort the data frame by column A1 such that the order of
  elements in A1 is as the same as in vec.



 After the ordering, the data frame would be


 A1   A2


 C 3


 A 2


 B 1




 Any suggestions would be appreciated.




 Thanks in advance




 Jeff



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 --
 -
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 Lawrence Livermore National Laboratory
 Livermore, CA, USA
 925-423-1062
 m...@llnl.gov -




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Re: [R] Replying to Posts Within Same Thread

2009-12-02 Thread James W. MacDonald

Whether or not your reply is threaded can also be due to the client you
use (if you use an email client). For instance, this reply will be
threaded correctly because I used Thunderbird. However, had I used my
university-approved Groupwise client it would appear as a new thread.

Best,

Jim

David Winsemius wrote:

On Dec 1, 2009, at 10:42 PM, Charlotte Maia wrote:

On 12/2/09, John Sorkin jsor...@grecc.umaryland.edu wrote:
I don't know what you are doing wrong because I don't know exactly
what you are doing. I do know that I don't have your problem when I
simply reply to a message without touching the subject line.

John

Could you clarify the notion of simply reply.
There is no obvious reply links in either the archive page, or the
digest.

True. The archive does not expose the message headers. I have not
figured out whether is is even possible to respond to a message on the
Archive. Some people use Gmane or Nabble, but I think most use a
mail-client. Responding to the digest can break threads.

In the case, where someone sends me an email, such have you have done,
I can simply reply.

However, in general this option is not available.

I am wondering why it wouldn't be? This particular message is threaded
with the posting you made a little over an hour ago, whereas some of
your replies in the last few days have been orphaned from the posting
you responded to (as you have noticed). You can look at the threaded
archive here (as I suspect you already know):

https://stat.ethz.ch/pipermail/r-help/

Best

--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: [R] Aligning Diagonally Oriented Labels Under Bar Chart

2009-12-02 Thread Jason Rupert



Peter, 

Thank you for your reply. 

That got me a lot closer.  Now I just need to move the text down a bit and it 
will be perfect.  

Thank you for your suggestion of creating a reference to barplot and passing 
that as an argument into text.  

That seems to have made the difference.  

Here is what I've ended up with so far:

#  Reference the following URL for information about rotating axis labels:
#  
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-rotated-axis-labels_003f
# mar A numerical vector of the form c(bottom, left, top, right) which gives 
the number of lines 
# of margin to be specified on the four sides of the plot. The default is c(5, 
4, 4, 2) + 0.1. 
par(mar = c(7, 4, 4, 2) + 0.1)
barplot_reference-barplot(WorldPhones[1,], 
    ylim=c(0, 5),
    axes=FALSE, ann=FALSE, 
    col=terrain.colors(length(WorldPhones[1,])), 
    xaxt = n,  xlab = )
# xpd  A logical value or NA. If FALSE, all plotting is clipped to the plot 
region, if TRUE, 
# all plotting is clipped to the figure region, and if NA, all plotting is 
clipped to 
# the device region.
    
text(barplot_reference, par(usr)[3] - 0.25, srt = 45, adj = 1,
 labels = as.character(colnames(WorldPhones)), xpd = TRUE)

#axis(1, at = barplot_reference, labels = as.character(colnames(WorldPhones)), 
srt = 45, adj = 1) 
box()



Any suggestions on adjusting the text down a bit is also greatly appreciated. 

Thank you again. 



 


- Original Message 
From: Peter Alspach peter.alsp...@plantandfood.co.nz
To: Jason Rupert jasonkrup...@yahoo.com; R-help@r-project.org
Sent: Tue, December 1, 2009 5:29:17 PM
Subject: RE: [R] Aligning Diagonally Oriented Labels Under Bar Chart

Tena koe Jason

Is this an example of what you want?

temp - barplot(3:17)
text(temp, rep(-0.5, length(3:17)), LETTERS[3:17], srt=45, adj=1)

HTH 

Peter Alspach 

 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Jason Rupert
 Sent: Wednesday, 2 December 2009 12:16 p.m.
 To: R-help@r-project.org
 Subject: [R] Aligning Diagonally Oriented Labels Under Bar Chart
 
 I searched the forms (i.e., R Search) and come up with the 
 following suggested link:
  
 http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-
 rotated-axis-labels_003f
 
 I tried to implement what I believe was being implied by that 
 URL and came up with the below:
 
 barplot(WorldPhones[1,],
     ylim=c(0, 5),
     axes=FALSE, ann=FALSE,
     col=terrain.colors(length(WorldPhones[1,])),
     xaxt = n,  xlab = )
 
 text(1:dim(WorldPhones)[1], par(usr)[3] - 0.1, srt = 45, adj = 1,
  labels = as.character(colnames(WorldPhones)), xpd = TRUE)
 
 box()
 
 
 Unfortunately the labels are not aligned with the appropriate 
 bars.  I believe I am missing something small in order to 
 have the text properly aligned underneath the appropriate bars.   
 
 Are there any suggestions for correcting this mis-alignment?  
 
 Thank you again for any additional feedback, links, hints or 
 insights.  
 
 
 
 
 __
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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 





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[R] Generate missing data patterns

2009-12-02 Thread Andreas Wittmann


Dear R-users,

i try to generate missing values in a matrix X according to a given 
missingnes pattern R with the probabilities p per row.


X-matrix(rnorm(3*100),ncol=3)

## indicator matrix for missingnes (1 observed, 0 missing)
R-matrix(c(1,1,1,
   0,0,1,
   1,1,0,
   0,1,1),ncol=3,byrow=TRUE)

## probabilities for row 1, row 2, row 3 and row 4
p-c(0.375,0.25,0.25,0.125)

## does not exactly what i want, because i get rows
## of missinges pattern which are not in R
X[rbinom(100,1,p[1])==1,R[1,]==1] - NA
X[rbinom(100,1,p[2])==1,R[2,]==1] - NA
X[rbinom(100,1,p[3])==1,R[3,]==1] - NA
X[rbinom(100,1,p[4])==1,R[4,]==1] - NA

So it would be great if i can get any advice how to do this. I also 
tried rmultinom or sample but without any success so far.


Another question is what to to if want the missing pattern R and 
simulate a certain amount of missingnes mybe about 10 %? I guess i have 
to mix the probabilities for each row in such a way to get approximatly 
the wanted missingnes in percent.


best regards

Andreas

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[R] find the index of the next largest element in a sorted vector

2009-12-02 Thread Hao Cen

Hi,

How can I find the index of the next largest element in a sorted vector if
an element is not found.

for example, searching 2 in c(0,3,4) would return 1 since 2 is not in the
vector and 0 is the next largest element to 2.

I tried which and match and neither returns such information.

 which(c(0,3,4) == 2)
integer(0)
 match(2, c(0,3,4))
[1] NA


thanks

Jeff

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Re: [R] plotting two surfaces simultaneously in a single panel

2009-12-02 Thread Deepayan Sarkar

On Fri, Nov 27, 2009 at 6:14 PM, Umesh Srinivasan
umesh.sriniva...@gmail.com wrote:
 Hi,

 I have recently begun using the lattice package, and have been using
 the wireframe command to visualise matrices which are model outputs. I
 have been trying to plot two surfaces (from two matrices)
 simultaneously in one panel, to visualise intersections etc., but
 neither my attempts or trawling the net are helping me find how to do
 this.

The documentation for wireframe mentions the use of 'groups' to do
this, and the usual shortcut of using formulae of the form z1+z2 ~ x +
y also works. The following seems to work as expected, subject to
caveats mentioned in ?wireframe and ?panel.wireframe (there is no
hidden surface removal going on, so intersections will not be shown
correctly).

df - as.data.frame.table(volcano)
names(df) - c(x, y, height)
df$sheight - scale(df$height)

wireframe(sheight + (-sheight) ~ x + y, df, aspect = c(1, .5))

-Deepayan

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Re: [R] Passing additional argument to be numerically integrated function

You may have hidden your posting by responding to an unrelated thread.  
(Avoid that in the future.) You need to be looking at:


?function   #and associated topics

This will drop you into a discussion that may be germane to your task:

http://finzi.psych.upenn.edu/Rhelp08/2009-April/194648.html

The above link was found with:

RSiteSearch(match args)

(There is a function named match.arg, whose precise spelling I had  
forgotten.)


--
David
On Dec 1, 2009, at 8:46 PM, Amir Liu wrote:




Hi,

I try to use the numerical integration functionality of R to  
integrate a univariate (1D) function. Below I am integrating  
function const1 which works nicely as expected. But for some reasons  
I need to pass to my function that I want to integrate an additional  
parameter. If it were object-oriented I just would invoke some  
setter methods onto a object providing functionality described in  
function constX and then pass this object on. And according to the  
help page the function can have more than one argument, just the  
first needs to be the argument vector for the integration function:


- f: an R function taking a numeric first argument and returning a  
numeric vector of the same length.  Returning a non-finite element  
will generate an error.


But let us say I have an additional argument called nb that I want  
to pass as well. How would I pass this second argument (and possibly  
more additional arguments) to make case 2 work, i.e. how this is  
expressed in R syntax?



integ - function() {

  # case 1: no argument for function to be integrated
  # integrate box function of height 1 from 0 to 2
  val - integrate(const1,0,2)
  print(val)

  # case 2: one ore more argument for function to be integrated
  # integrate box function of height nb from 0 to 2
  nb - 5
  val1 - integrate(constX,0,2)
  print(val1)

}

const1 - function(x) {
 return(rep(1,length(x)))
}

constX - function(x,nb) {
 return(rep(nb,length(nb)))
}


Kind Regards,

Amir
--



David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Aligning Diagonally Oriented Labels Under Bar Chart


Pasting a few trailing spaces worked for me.

On Dec 2, 2009, at 9:29 AM, Jason Rupert wrote:




Peter,

Thank you for your reply.

That got me a lot closer.  Now I just need to move the text down a  
bit and it will be perfect.


Thank you for your suggestion of creating a reference to barplot and  
passing that as an argument into text.


That seems to have made the difference.

Here is what I've ended up with so far:

#  Reference the following URL for information about rotating axis  
labels:

#  
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-rotated-axis-labels_003f
# mar A numerical vector of the form c(bottom, left, top, right)  
which gives the number of lines
# of margin to be specified on the four sides of the plot. The  
default is c(5, 4, 4, 2) + 0.1.

par(mar = c(7, 4, 4, 2) + 0.1)
barplot_reference-barplot(WorldPhones[1,],
ylim=c(0, 5),
axes=FALSE, ann=FALSE,
col=terrain.colors(length(WorldPhones[1,])),
xaxt = n,  xlab = )
# xpd  A logical value or NA. If FALSE, all plotting is clipped to  
the plot region, if TRUE,
# all plotting is clipped to the figure region, and if NA, all  
plotting is clipped to

# the device region.

text(barplot_reference, par(usr)[3] - 0.25, srt = 45, adj = 1,
 labels = as.character(colnames(WorldPhones)), xpd = TRUE)

#axis(1, at = barplot_reference, labels =  
as.character(colnames(WorldPhones)), srt = 45, adj = 1)

box()



Any suggestions on adjusting the text down a bit is also greatly  
appreciated.


Thank you again.






- Original Message 
From: Peter Alspach peter.alsp...@plantandfood.co.nz
To: Jason Rupert jasonkrup...@yahoo.com; R-help@r-project.org
Sent: Tue, December 1, 2009 5:29:17 PM
Subject: RE: [R] Aligning Diagonally Oriented Labels Under Bar Chart

Tena koe Jason

Is this an example of what you want?

temp - barplot(3:17)
text(temp, rep(-0.5, length(3:17)), LETTERS[3:17], srt=45, adj=1)

HTH 

Peter Alspach


-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jason Rupert
Sent: Wednesday, 2 December 2009 12:16 p.m.
To: R-help@r-project.org
Subject: [R] Aligning Diagonally Oriented Labels Under Bar Chart

I searched the forms (i.e., R Search) and come up with the
following suggested link:

http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-
rotated-axis-labels_003f

I tried to implement what I believe was being implied by that
URL and came up with the below:

barplot(WorldPhones[1,],
ylim=c(0, 5),
axes=FALSE, ann=FALSE,
col=terrain.colors(length(WorldPhones[1,])),
xaxt = n,  xlab = )

text(1:dim(WorldPhones)[1], par(usr)[3] - 0.1, srt = 45, adj = 1,
 labels = as.character(colnames(WorldPhones)), xpd = TRUE)

box()


Unfortunately the labels are not aligned with the appropriate
bars.  I believe I am missing something small in order to
have the text properly aligned underneath the appropriate bars.

Are there any suggestions for correcting this mis-alignment?

Thank you again for any additional feedback, links, hints or
insights.




__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.







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and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] find the index of the next largest element in a sorted vector



On Dec 2, 2009, at 9:34 AM, Hao Cen wrote:


Hi,

How can I find the index of the next largest element in a sorted  
vector if

an element is not found.

for example, searching 2 in c(0,3,4) would return 1 since 2 is not  
in the

vector and 0 is the next largest element to 2.

I tried which and match and neither returns such information.


which(c(0,3,4) == 2)

integer(0)

match(2, c(0,3,4))

[1] NA


Take a look at these. I changed to problem so that the answer would  
be in the middle of the sequence.


 which(c(0,3,4) = 2)
[1] 1   # but which would have retruned several values if the match  
were in the middle

 which(c(-3,-1, 0,3,4) = 2)
[1] 1 2 3
 tail(which(c(-3,-1,0,3,4) = 2),1)
[1] 3  # the desired index

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] find the index of the next largest element in a sorted vector

2009-12-02 Thread jim holtman

Is this what you want:

 x - c(0,3,4)
 ?findInterval
 findInterval(2, x)
[1] 1



On Wed, Dec 2, 2009 at 9:34 AM, Hao Cen h...@andrew.cmu.edu wrote:
 Hi,

 How can I find the index of the next largest element in a sorted vector if
 an element is not found.

 for example, searching 2 in c(0,3,4) would return 1 since 2 is not in the
 vector and 0 is the next largest element to 2.

 I tried which and match and neither returns such information.

 which(c(0,3,4) == 2)
 integer(0)
 match(2, c(0,3,4))
 [1] NA


 thanks

 Jeff

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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Re: [R] How to export a function from a package and access it only by specifying the namespace?

2009-12-02 Thread Peng Yu

On Tue, Dec 1, 2009 at 11:27 PM, Sharpie ch...@sharpsteen.net wrote:


 Peng Yu wrote:

 Then I try the package 'try.package' in an R session. I'm wondering
 why neither 'my_test_f' and 'try.package::my_test_f' work.


 The error message you got below clearly explains this-- you did not export
 my_test_f in your NAMESPACE file.  To access unexported functions, you must
 use the ':::' operator:

  try.package:::my_test_f()



 Peng Yu wrote:

 Why 'my_test_g' can be accessed with 'try.package::' and without
 'try.package::'?


 Because you exported it in the NAMESPACE file.



 Peng Yu wrote:

 Is there a way to make  'my_test_g' accessible only by specifying the
 namespace 'try.package::'?


 No.

 The purpose of the '::' operator is for those cases where multiple packages
 are loaded that each export a function with the same name.  This is known as
 masking and the last loaded package will contribute the dominant
 function-- i.e. the function the gets called when the user types
 functionName() and not packageName::functionName().  The :: operator
 allows the selection of functions that are masked by the dominant function.

 If you really want to conceal a function from user-level code, don't export
 it and it will only be accessible via the ::: operator.

Is there a way to list all the functions in a namespace? I tried the
following one, but it is not working.

 showMethods(where=getNamespace('try.package'))
No applicable functions

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Re: [R] A ggplot question

2009-12-02 Thread Matthieu Dubois

Hi Megh, 

just set the legned position to 'none' using options, by putting
 + opts(legend.position=none) after your code. 

ggplot(diamonds, aes(carat, ..density..)) + 
geom_histogram(binwidth = 0.2, aes(fill = cut)) + 
facet_grid(. ~ cut) + 
opts(legend.position=none)

HTH, 

Matthieu

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[R] Ridge regression

2009-12-02 Thread Eleni Christodoulou

Dear list,

I have a couple of questions concerning ridge regression. I am using the
lm.ridge(...) function in order to fit a model to my microarray data.
Thus *model=lm.ridge(...)*
I retrieve some coefficients and some scales for each gene. First of all, I
would like to ask: the real coefficients of the model are not included in
the first argument of the output but in the result of coef(model), am I
right? Moreover, what does the scale argument represent? Which is its
connection with the coefficients? The R help file os not very informative
for me...

Thank you very much in advance,
Eleni Christodoulou

[[alternative HTML version deleted]]

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Re: [R] Problem with Cannot compute correct p-values with ties

2009-12-02 Thread Zhijiang Wang


   I am sorry that I didn't express my question more clearly and made you
   understand it so difficult.
   But thank you all your kind help very much and I have used another method
   for solving it.
   Thank you all again!
   [1]guohao.hu...@gmail.com åé:

Please try to find answers by yourself
You should not just post problems without thinking them.


 Huang, Guo-Hao

--
From: Zhijiang Wang [2]ivoryto...@emails.bjut.edu.cn
Sent: Wednesday, December 02, 2009 4:52 PM
To: [3]R-help@r-project.org
Subject: [R] Problem with Cannot compute correct p-values with ties


   Dear All,
   1. why did the problem happen?
   2. How to solve it?

   --

Best wishes,
Zhijiang Wang

PHD Student
Room 212, Science buliding,
The International WIC Institute,
College of Computer Science and Technology,
Beijing University of Technology,
Beijing, China.
__
[4]r-h...@r-project.org mailing list
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PLEASE do read the posting guide [6]http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




   --

Best wishes,
Zhijiang Wang

PHD Student
Room 212, Science buliding,
The International WIC Institute,
College of Computer Science and Technology,
Beijing University of Technology,
Beijing, China.

References

   1. mailto:guohao.hu...@gmail.com
   2. mailto:ivoryto...@emails.bjut.edu.cn
   3. mailto:R-help@r-project.org
   4. mailto:R-help@r-project.org
   5. https://stat.ethz.ch/mailman/listinfo/r-help
   6. http://www.R-project.org/posting-guide.html
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Ridge regression



On Dec 2, 2009, at 10:42 AM, Eleni Christodoulou wrote:


Dear list,

I have a couple of questions concerning ridge regression. I am using  
the

lm.ridge(...) function in order to fit a model to my microarray data.
Thus *model=lm.ridge(...)*
I retrieve some coefficients and some scales for each gene. First of  
all, I
would like to ask: the real coefficients of the model are not  
included in
the first argument of the output but in the result of coef(model),  
am I

right?


Not exactly. coef(model) extracts the coefficients from the model but  
the coefficients do in the example instance I created following the  
help page happen to be in the first element of the model.


eg:
 long.rr$coef
 GNP   Unemployed Armed.Forces   Population Year  
Employed
  25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825

 long.rr[[1]]
 GNP   Unemployed Armed.Forces   Population Year  
Employed
  25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825



Moreover, what does the scale argument represent? Which is its
connection with the coefficients? The R help file os not very  
informative

for me...


A plausible response to such a question might be that the help page is  
a sketchy substitute for the MASS book. However, I cannot find ridge  
regression in the table of contents or in the index of my copy, but I  
only have ed. 2 and the current edition is the 4th. So we will both  
need to wait for more knowledgeable (or with more recent editions of  
MASS) persons to answer that question.


(And scales is not an argument, rather it's a returned value.)



Thank you very much in advance,
Eleni Christodoulou




David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] standardized beta weights for lmer models

2009-12-02 Thread Annett Jorschick

Dear Sir or Madam,

I am using the lme4 package to model the effect of various variables on 
binomial response data in a repeated measurements design. Besides the 
significance of the main predictors, we are also interested in the size and 
direction of the (partial) correlation of the predictors with the dependent 
variable.  Therefore, we wonder whether the estimates listed under 
coefficients in the model summary are standardized or not. Could you inform 
us about this? And if they are not standardized, is there a way (or package) to 
calculate the standardized beta-weights and/or the partial correlations 
belonging to the predictor variables in logit lmer models? 

Thank you very much for your help.

Best regards,
Annett

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Re: [R] Ridge regression



On Dec 2, 2009, at 11:04 AM, David Winsemius wrote:



On Dec 2, 2009, at 10:42 AM, Eleni Christodoulou wrote:


Dear list,

I have a couple of questions concerning ridge regression. I am  
using the

lm.ridge(...) function in order to fit a model to my microarray data.
Thus *model=lm.ridge(...)*
I retrieve some coefficients and some scales for each gene. First  
of all, I
would like to ask: the real coefficients of the model are not  
included in
the first argument of the output but in the result of coef(model),  
am I

right?


Not exactly. coef(model) extracts the coefficients from the model  
but the coefficients do in the example instance I created following  
the help page happen to be in the first element of the model.


eg:
 long.rr$coef
GNP   Unemployed Armed.Forces   Population Year  
Employed
 25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825

 long.rr[[1]]
GNP   Unemployed Armed.Forces   Population Year  
Employed
 25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825



Moreover, what does the scale argument represent? Which is its
connection with the coefficients? The R help file os not very  
informative

for me...


A plausible response to such a question might be that the help page  
is a sketchy substitute for the MASS book. However, I cannot find  
ridge regression in the table of contents or in the index of my  
copy, but I only have ed. 2 and the current edition is the 4th. So  
we will both need to wait for more knowledgeable (or with more  
recent editions of MASS) persons to answer that question.


After a bit more searching, I am thinking that the 4th edition may not  
be teh source for answers. It appears that lm.ridge is a worked answer  
to one of hte questions at the back of chapter 6. See p 6 and 24 (in  
the pdf numbering):


http://www.stats.ox.ac.uk/pub/MASS4/VR4ex.pdf



(And scales is not an argument, rather it's a returned value.)



Thank you very much in advance,
Eleni Christodoulou




David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] lattice: adding information on number of observations

2009-12-02 Thread RICHARD M. HEIBERGER

The boxplot with sample size information is one of the features
included in the HH package.
An example is posted on my site
http://astro.ocis.temple.edu/~rmh/HH/bwplot-color.pdf

In this example I show grouping, control of x-axis position, multiple
x-axis labels, and
control of display of extreme outliers.

Rich

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Re: [R] Extract html tables to data.frames

2009-12-02 Thread Henrique Dallazuanna

See readHTMLTable in XML package.

On Wed, Dec 2, 2009 at 2:14 PM, Daniel Brewer daniel.bre...@icr.ac.uk wrote:
 Hello,

 I would like to scrape some html tables from a web page and convert them
 to a data.frame so I can perform further analysis.  Could anyone tell me
 the best way to do this?  Would it be more appropriate to use an
 external tool first?

 Thanks

 Dan

 --
 **
 Daniel Brewer, Ph.D.

 Institute of Cancer Research
 Molecular Carcinogenesis
 Email: daniel.bre...@icr.ac.uk
 **

 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
 Limited by Guarantee, Registered in England under Company No. 534147 with its 
 Registered Office at 123 Old Brompton Road, London SW7 3RP.

 This e-mail message is confidential and for use by the a...{{dropped:2}}

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Re: [R] problems installing R packages

2009-12-02 Thread Héctor Villalobos

Try to install your old R version in a non system folder (like C:/R/R-2.4.0)

Correct me if I'm wrong, but I believe that in vista you can't install packages 
in a system
folder ('C:/Program Files/R/R-2.4.0) even if you have administrator 
privileges...

Héctor



On 2 Dec 2009 at 3:55, catuxa-2 wrote:

Date sent:  Wed, 2 Dec 2009 03:55:21 -0800 (PST)
From:   catuxa-2 catuxa...@gmail.com
To: r-help@r-project.org
Subject:[R]  problems installing R packages


 Hi,
 I´m trying to install new package in R (version 2.4.0) under windows vista
 and i have problems. I always receive the same message:
 Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
 'C:/Program Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
 It can´t open the file.
 I check the compatibility with the version and is ok, I have no idea where's
 the problem cause i'm the administrator and i've enough free space in the
 hard disc.

 Anyone could help me

 --
 View this message in context: 
 http://n4.nabble.com/problems-installing-R-packages-tp933010p933010.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


--
Héctor Villalobos hvill...@ipn.mx
 CICIMAR - IPN
 A.P. 592. Col. Centro
 La Paz, Baja California Sur, MÉXICO. 23000
 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34  ext. 82425
 Fax.  (+52 612) 122 53 22

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Re: [R] problems installing R packages




Héctor Villalobos wrote:

Try to install your old R version in a non system folder (like C:/R/R-2.4.0)

Correct me if I'm wrong, but I believe that in vista you can't install packages 
in a system
folder ('C:/Program Files/R/R-2.4.0) even if you have administrator 
privileges...


In that case nobody could install anything. No, you can, but you really 
need the privileges, i.e. right click on startup of R and tell the OS to 
start R really with Admin privieges.


Uwe Ligges






Héctor



On 2 Dec 2009 at 3:55, catuxa-2 wrote:

Date sent:  Wed, 2 Dec 2009 03:55:21 -0800 (PST)
From:   catuxa-2 catuxa...@gmail.com
To: r-help@r-project.org
Subject:[R]  problems installing R packages


Hi,
I´m trying to install new package in R (version 2.4.0) under windows vista
and i have problems. I always receive the same message:
Erro en zip.unpack(pkg, tmpDir) : no fue posible abrir el archivo
'C:/Program Files/R/R-2.4.0/library/file2019500d/mprobit/libs/mprobit.dll'
It can´t open the file.
I check the compatibility with the version and is ok, I have no idea where's
the problem cause i'm the administrator and i've enough free space in the
hard disc.

Anyone could help me

--
View this message in context: 
http://n4.nabble.com/problems-installing-R-packages-tp933010p933010.html
Sent from the R help mailing list archive at Nabble.com.

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and provide commented, minimal, self-contained, reproducible code.



--
Héctor Villalobos hvill...@ipn.mx
 CICIMAR - IPN
 A.P. 592. Col. Centro
 La Paz, Baja California Sur, MÉXICO. 23000
 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34  ext. 82425
 Fax.  (+52 612) 122 53 22

[[alternative HTML version deleted]]





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Re: [R] Starting estimates for nls Exponential Fit

2009-12-02 Thread Prof. John C Nash

Kate Mullen showed one approach to this problem by using DEOptim to get
some good starting values.

However, I believe that the real issue is scaling (Warning: well-ridden
hobby-horse!).

With appropriate scaling, as below, nls does fine. This isn't saying nls
is perfect -- I've been trying to figure out how to do a nice job of
helping folk to scale their problems. Ultimately, it would be nice to
has an nls version that will do the scaling and also watch for some
other situations that give trouble.

Cheers, JN


## JN test
rm(list=ls())

ExponValues - c(2018.34,2012.54,2018.85,2023.52,2054.58,2132.61,2247.17,
 2468.32,2778.47)

ExponCycles - c(17,18,19,20,21,22,23,24,25)

mod - function(x) x[1] + x[2]*x[3]^ExponCycles

modj - function(x) (1000*x[1] + 0.001*x[2]*x[3]^ExponCycles)

fun - function(x) sum((ExponValues-mod(x))^2)



pa-c(1,2,3)
lo-c(0,0,0)
up-c(20,20,20)
names(pa) - c(Y0, a, E)

## fit w/port and GN
Emodjn- nls(ExponValues ~ (1000*Y0 + 0.001*a*(E^ExponCycles)),
 start=pa, algorithm='port', lower=lo, upper=up,
 control=list(maxiter=1000, trace=TRUE, warnOnly=TRUE))

Emodjn1 - nls(ExponValues ~ (1000*Y0 + 0.001*a*(E^ExponCycles)), start=pa,
 control=list(maxiter=1000, trace=TRUE, warnOnly=TRUE))

## fit
matplot(cbind(ExponValues, fitted(Emodjn), fitted(Emodjn1)),type=l)

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Re: [R] pictures_in_a_matrix




Claudia Hantschel wrote:

Dear all,
how is it possible to upload first two figures (original: jpeg files, 
these are two pictures from a micrope) in a layout(matrix(c(1,2,3), 
1,3), widths=c(2.5,1.5, 2.5), heights=c(1,1) ) (the last field of the 
matrix is for a barplot)? The hole matrix is then need to be safed as 
eps-format. Does it make sense to upload these figures in R?

Many thanks for any help! Claudia.



I am not sure if it makes much sense to load the pictures into R just to 
print them again. But if you really want to do it that way, see the book 
on R Graphics by Paul Murrell or his slides from useR! 2006:

http://www.stat.auckland.ac.nz/~paul/Talks/rgraphs.pdf

Best,
Uwe Ligges

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[R] Arithmetic on multiple files

2009-12-02 Thread Muhammad Rahiz


Dear R-users,

I'd like to perform arithmetic functions on 1000 files containing a 
2000x2000 matrix. Can anyone advise?


For example,

File1File2   Output
1 1 1   4 4 4   5 5 5
2 2 2 +5 5 5= 7 7 7
3 3 3   6 6 6   9 9 9



Muhammad

--
Muhammad Rahiz  |  Doctoral Student in Regional Climate Modeling

Climate Research Laboratory, School of Geography  the Environment  
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom 
Tel: +44 (0)1865-285194	 Mobile: +44 (0)7854-625974

Email: muhammad.ra...@ouce.ox.ac.uk

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Re: [R] go back a block of code in history




Peng Yu wrote:

Suppose I run the following code in the R session. At the last prompt
'', I want to retrieve the second command (staring with 'y'). But I
have to type up arrow many times, which is very inconvenient. I'm
wondering if there is a way to configure R to skip block of code in
the history?


I don't think so, but since you are writing your code in an editor 
(hopefully), it is probably easier to submit the relevant part of the 
code from the editor to R again.


Uwe Ligges







x=list(a=c(1,2),b=c(3,4,5))
y=list(a=c(1,2),b=c(3,4,5))
lapply(seq(along=x)

+ ,function(i){
+   cbind(
+   x[[i]]
+   ,y[[i]]
+   )
+ }
+ )
[[1]]
 [,1] [,2]
[1,]11
[2,]22

[[2]]
 [,1] [,2]
[1,]33
[2,]44
[3,]55


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Re: [R] Arithmetic on multiple files


About this:

foo - function( files = c( file1, file2 ), nr = 3, nc = 3 ){
  out - numeric( nr * nc )
  for( i in seq_along(files)){
out - out + scan( files[i] , what = numeric(0), quiet = TRUE )
  }
  matrix( out, nr = nr, nc = nc, byrow = T )
}

 foo()
 [,1] [,2] [,3]
[1,]555
[2,]777
[3,]999


This would have been more fun if you could store them all in memory at 
once (which I think you can't) :


 files - c(file1, file2 )
 matrices - lapply( files, scan, what = numeric(0), quiet = TRUE )
 matrix( Reduce( +, matrices ), nr = 3, nc = 3, byrow = TRUE )
 [,1] [,2] [,3]
[1,]555
[2,]777
[3,]999

Romain


On 12/02/2009 05:53 PM, Muhammad Rahiz wrote:


Dear R-users,

I'd like to perform arithmetic functions on 1000 files containing a
2000x2000 matrix. Can anyone advise?

For example,

File1 File2 Output
1 1 1 4 4 4 5 5 5
2 2 2 + 5 5 5 = 7 7 7
3 3 3 6 6 6 9 9 9



Muhammad




--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/Gq7i : ohloh
|- http://tr.im/FtUu : new package : highlight
`- http://tr.im/EAD5 : LondonR slides

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Re: [R] R script From PHP

How do I check whether R bin directory is added to PATH variable or not and
if not then how do i add it?

On Wed, Dec 2, 2009 at 5:34 PM, Romain Francois
romain.franc...@dbmail.comwrote:

 On 12/02/2009 12:30 PM, Hrishi Mittal wrote:



 I agree with Romain that you should probably try and get Rserve to work as
 that is a much better way. However, to get your commandline version
 working,
 I suggest you use the Rscript comman instead of a bash script. So let's
 say
 you save your R script as a myscript.R file. Then do:

 shell_exec('Rscript /path/to/myscript.R'. 21);

 If that still gives you an error like Rscript command not found, then you
 need to make sure your R bin directory is added to the PATH system
 variable.


 ... maybe shell_exec('/usr/bin/Rscript /path/to/myscript.R'. 21);


 --
 Romain Francois
 Professional R Enthusiast
 +33(0) 6 28 91 30 30
 http://romainfrancois.blog.free.fr
 |- http://tr.im/FtUu : new package : highlight
 |- http://tr.im/EAD5 : LondonR slides
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Re: [R] Ridge regression

2009-12-02 Thread Ravi Varadhan

You are right that the ans$coef and coef(ans) are different in ridge
regression, where `ans' is the object from lm.ridge.  It is the coef(ans)
that yields the coefficients on the original scale.  ans$coef is the
coefficient of X-scaled and Y-centered version.

Here is an example that illustrates the workings of ridge regression.

First let us create some data:

X1 - runif(20)
X2 - runif(20)
Y - 2 * X1 - 2 * X2 + rnorm(20, sd=0.1)

lam - 10
ans1 - lm.ridge(Y ~ X1 + X2, lambda = lam)
ans1$coef
coef(ans1)
# Note that these two are different

# Now Let us scale the variables X1 and X2 and center Y
#
cY - scale(Y, scale=FALSE) 
n - length(Y)
sX1 - scale(X1) * sqrt(n/(n-1)) 
sX2 - scale(X2) *  sqrt(n/(n-1))

require(MASS)

lam - 10
ans2 - lm.ridge(cY ~ sX1 + sX2, lambda = lam)

ans2$coef
coef(ans2)
# Now, see that the coefficients of sX1 and sX2 are the same
# This is the connection!

# Armed with this insight, we now compare the ans1$coef with scaled
coefficients
#
ans1$coef
c(coef(ans1)[2] * sd(X1), coef(ans1)[3] * sd(X2)) * sqrt((n-1)/n)

# Now they are the same!

I hope this is clear.

Best,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 




-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Winsemius
Sent: Wednesday, December 02, 2009 11:04 AM
To: Eleni Christodoulou
Cc: r-help@r-project.org
Subject: Re: [R] Ridge regression


On Dec 2, 2009, at 10:42 AM, Eleni Christodoulou wrote:

 Dear list,

 I have a couple of questions concerning ridge regression. I am using  
 the
 lm.ridge(...) function in order to fit a model to my microarray data.
 Thus *model=lm.ridge(...)*
 I retrieve some coefficients and some scales for each gene. First of  
 all, I
 would like to ask: the real coefficients of the model are not  
 included in
 the first argument of the output but in the result of coef(model),  
 am I
 right?

Not exactly. coef(model) extracts the coefficients from the model but  
the coefficients do in the example instance I created following the  
help page happen to be in the first element of the model.

eg:
  long.rr$coef
  GNP   Unemployed Armed.Forces   Population Year  
Employed
   25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825
  long.rr[[1]]
  GNP   Unemployed Armed.Forces   Population Year  
Employed
   25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825

 Moreover, what does the scale argument represent? Which is its
 connection with the coefficients? The R help file os not very  
 informative
 for me...

A plausible response to such a question might be that the help page is  
a sketchy substitute for the MASS book. However, I cannot find ridge  
regression in the table of contents or in the index of my copy, but I  
only have ed. 2 and the current edition is the 4th. So we will both  
need to wait for more knowledgeable (or with more recent editions of  
MASS) persons to answer that question.

(And scales is not an argument, rather it's a returned value.)


 Thank you very much in advance,
 Eleni Christodoulou



David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] How to export a function from a package and access it only by specifying the namespace?

2009-12-02 Thread Sharpie



Peng Yu wrote:
 
 Is there a way to list all the functions in a namespace? I tried the
 following one, but it is not working.
 
 showMethods(where=getNamespace('try.package'))
 No applicable functions
 


See:

  http://n4.nabble.com/Check-functions-in-package-td894903.html#a894905
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View this message in context: 
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Re: [R] polygon graph

2009-12-02 Thread Peter Ehlers



Jose Narillos de Santos wrote:

Hi all,

I have a matrix dd with dates and data. i WANT to create a grpah with shade
between the line and the zero axis. I´m trying to use polygon but something
doesn´ t work

Imagine.

I want to plot

g-read.table(dd.txt, col.names=c(fecha,DP))

g$fecha - as.Date(g$fecha, format=%d/%m/%Y)

t-g$fecha
st-length(g$DP)

ft-plot(t,g$DP,type=l,ylab=DP)

polygon(c(1, 1:st, st), c(0, g$USGDP, 0), col = blue)

abline(h = 0, lwd = 1, col = black)

If I ommit ploygon line the doc works properly (it plots a graph line).

But I want to colur the area below or over the line and the zero axis.

Can you guide or indicate because in this case polygon doesn´t work.

I attach the two files.


(You need to get your variable names straight: DP, not USGDP)
As you have it, polygon is looking for values 1:28 on the x-axis.
It won't find them:

 par('usr')

will tell you what the range of x-values is on the plot.

Change your line to:

 polygon(c(t[1],t,t[st]), c(0, g$DP, 0), col = blue)

This should work (untested).

 -Peter Ehlers




Thanks in advance for all.




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Re: [R] Plotting an interaction with error bars

2009-12-02 Thread Dror D Lev

Hello Jim,

I have encountered a puzzling pattern of results using brkdn.plot():

 brkdn.plot(Duration,group_val,blck,data=dpp)
$mean
 [,1]  [,2] [,3]  [,4]
[1,] 0.653842 0.5679849 0.477645 0.4250087
[2,] 0.653842 0.5679849 0.477645 0.4250087
[3,] 0.653842 0.5679849 0.477645 0.4250087
[4,] 0.653842 0.5679849 0.477645 0.4250087
[5,] 0.653842 0.5679849 0.477645 0.4250087

(I've omitted the $std.error matrix to save space since the pattern is the
same)

To verify the pattern of repetitions is not in my data I made another
calculation and there is no pattern of repetition:

 with(dpp, ftable(by(Duration,list(group_val,blck),mean,na.rm=T)))
   1 2 3 4

0.015  0.7493519 0.5125178 0.4538040 0.3498578
0.02   0.5583320 0.6234520 0.5014860 0.5001596
0.028  0.5446862 0.3600077 0.2951988 0.2842502
0.035  0.4396780 0.2335916 0.1992378 0.1661076
0.045  0.2711094 0.1305614 0.0969594 0.1491294

Is there a way to make brkdn.plot() to present this data?

Thank you,
dror

-

On Wed, Nov 4, 2009 at 12:21 PM, Dror D Lev dror.te...@gmail.com wrote:

 Indeed, that seems very convenient.
 Thanks for your work and for the help.

 dror

 -

 On Wed, Nov 4, 2009 at 12:17 PM, Jim Lemon j...@bitwrit.com.au wrote:
  On 11/04/2009 06:36 PM, Dror D Lev wrote:
 
  Thank you Jim.
 
  brkdn.plot() seems to be just the function I need.
 
  Still, I wonder if there are lists of labels of the different measures
  of central tendency (mct argument) and measures of dispersion (md)?
 
 
 
  Hi Dror,
  With brkdn.plot (and several other functions in plotrix) you can use any
  existing measure or even roll your own. The only limitation is that the
  function has to return a numeric value and must accept an na.rm
 argument.
 
  Jim
 
 


[[alternative HTML version deleted]]

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Re: [R] Adding and Multiplying two Unevaluated Expressions


Benjamin Müller wrote:

HI,

As I'm trying to compute Taylor series, I'm having problems in adding and 
multiplying unevaluated expressions. I searched for a solution but found none.

my Taylor function works fine for evaluating functions as you can see here:


rTaylorVal=function(exp,x0,dx,n) {

ls=list(x=x0)

newexp=eval(exp,ls)

exp0=exp

for (i in 1:n){
exp0=D(exp0,x)
newexp=newexp+eval(exp0,ls)/factorial(i)*dx^i
}

return(newexp)

}

Where exp is an expression like exp=expression(x^2*sin(x)), x0 is the 
startvalue, dx the difference between startvalue and searched value and n is 
the length of the series.

So I tried to remove dx as a value, to get a Taylor series expression, but it 
doesn't work as simple multiplication (*) and accumulation (+) is not good for 
expressions.

That's my point so far, now my question:

Is it actually possible to add and/or multiply expressions, and how?



Well, although R as a numerical language is not designed for these kind 
of things, you can do it, e.g. using a function


opExpr - function(expr1, expr2, op = +){
expr - expression(a + b)
expr[[1]][[1]] - as.name(op)
expr[[1]][[2]] - expr1[[1]]
expr[[1]][[3]] - expr2[[1]]
expr
}

that can construct such expressions as in:

opExpr(expression(x * sin(x)), expression(x^2 * sin(x)))
opExpr(expression(x * sin(x)), expression(x^2 * sin(x)), *)

Best wishes,
Uwe Ligges




Thank you so far.

Benjamin Müller
Geographer (B.Sc.)




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[R] Structural Equation Models(SEM)

2009-12-02 Thread Ralf Finne

Hi R-colleagues.

I have been using the sem(sem) function.  It uses
maximum likelyhood as optimizing. method.
According to simulation study in Umeå Sweden
(http://www.stat.umu.se/kursweb/vt07/stad04mom3/?download=UlfHolmberg.pdf
Sorry it is in swedish, except the abstract)
maximum likelihood is OK for large samples and normal distribution
the SEM-problem should be optimized by GLS (Generalized Least Squares).


So to the question:

Is there any R-function that solves SEM with GLS?


Ralf Finne
Novia University of Applied Science
Vasa  Finland

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[R] [Fwd: Re: Adding and Multiplying two Unevaluated Expressions]

2009-12-02 Thread Benjamin Müller




 Original-Nachricht 
Betreff:Re: [R] Adding and Multiplying two Unevaluated Expressions
Datum:  Tue, 01 Dec 2009 23:49:39 +0100
Von:Benjamin Müller ben_mueller...@web.de
An: Rolf Turner r.tur...@auckland.ac.nz
Referenzen: 	20091201144125.316...@gmx.net 
8e40e49f-e8fc-4fbd-8cc5-93789ffb0...@auckland.ac.nz




This works fine for your example, but doesn't work as simple if there's 
more than these expressions.


In my example this would be in line 11:

newexp=as.expression(substitute(a+con1/con2*b^con3,list(a=newexp[[1]],b=expression(dx)[[1]],con1=eval(exp0,ls),con2=factorial(i),con3=1*i)))

this works just fine and you can still evaluate this. thank you very much!

If there's an easier way, let me know.
Greets,
Ben Müller


Rolf Turner schrieb:


On 2/12/2009, at 3:41 AM, Benjamin Müller wrote:


HI,

As I'm trying to compute Taylor series, I'm having problems in adding 
and multiplying unevaluated expressions. I searched for a solution 
but found none.


my Taylor function works fine for evaluating functions as you can see 
here:



rTaylorVal=function(exp,x0,dx,n) {

ls=list(x=x0)

newexp=eval(exp,ls)

exp0=exp

for (i in 1:n){
exp0=D(exp0,x)
newexp=newexp+eval(exp0,ls)/factorial(i)*dx^i
}

return(newexp)

}

Where exp is an expression like exp=expression(x^2*sin(x)), x0 is the 
startvalue, dx the difference between startvalue and searched value 
and n is the length of the series.


So I tried to remove dx as a value, to get a Taylor series 
expression, but it doesn't work as simple multiplication (*) and 
accumulation (+) is not good for expressions.


That's my point so far, now my question:

Is it actually possible to add and/or multiply expressions, and how?


This may well be a case of the blind leading the partially sighted,
but for what it's worth my answer is ``Yes, but it's a kludge.''
One needs to use substitute, it seems to me.

E.g.:

e1 - expression((x+y)^2)
e2 - expression(1/(x^2 + y^2))
e3 - as.expression(substitute(a+b,list(a=e1[[1]],b=e2[[1]])))
e3
D(e3,x)
D(e3,y)

Older and wiser heads may provide you with better counsel.

cheers,

Rolf Turner




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Re: [R] Arithmetic on multiple files

2009-12-02 Thread Benjamin Müller

Ain't it as simple as load them (read() or read.csv()), add (+) 
these dataframes and thats all? you also can export them again with 
write().


greets,
Benjamin Müller

Muhammad Rahiz schrieb:

Dear R-users,

I'd like to perform arithmetic functions on 1000 files containing a 
2000x2000 matrix. Can anyone advise?


For example,

File1File2   Output
1 1 1   4 4 4   5 5 5
2 2 2 +5 5 5= 7 7 7
3 3 3   6 6 6   9 9 9



Muhammad



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[R] Reordering the results from table(cut()) by break argument

2009-12-02 Thread Mark Heckmann

I have a vector and need to count how many data points fall inside  
each bin:


dat - rnorm(100)
breaks - -3:3
table((cut(dat, breaks)))

(-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
  3  13  42  30  12   0

if I reverse the breaks vector, the results remains the same:
breaks - rev(breaks)
table((cut(dat, breaks)))

(-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
  3  13  42  30  12   0

What I would like is break to also determine the order of the table  
output, in this case it should also be reversed, like:

( 3, 2] ( 2, 1]  ( 1,0]   (0,-1]   (-1,-2]   (-2,-3]
  0  12  30  42  13   3

Thus I would like to reorder the vector using break, but I do not know  
how.


TIA
Mark
–––
Mark Heckmann
Dipl. Wirt.-Ing. cand. Psych.
Vorstraße 93 B01
28359 Bremen
Blog: www.markheckmann.de
R-Blog: http://ryouready.wordpress.com

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Re: [R] Reordering the results from table(cut()) by break argument

2009-12-02 Thread jim holtman

try this:

 dat - rnorm(100)
 breaks - -3:3
 table((cut(dat, breaks)))

(-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
  1  10  35  39  13   2
 x - table((cut(dat, breaks)))
 rev(x)

  (2,3]   (1,2]   (0,1]  (-1,0] (-2,-1] (-3,-2]
  2  13  39  35  10   1



On Wed, Dec 2, 2009 at 12:18 PM, Mark Heckmann mark.heckm...@gmx.de wrote:
 I have a vector and need to count how many data points fall inside each bin:

 dat - rnorm(100)
 breaks - -3:3
 table((cut(dat, breaks)))

 (-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
      3      13      42      30      12       0

 if I reverse the breaks vector, the results remains the same:
 breaks - rev(breaks)
 table((cut(dat, breaks)))

 (-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
      3      13      42      30      12       0

 What I would like is break to also determine the order of the table output,
 in this case it should also be reversed, like:
 ( 3, 2] ( 2, 1]  ( 1,0]   (0,-1]   (-1,-2]   (-2,-3]
      0      12      30      42      13       3

 Thus I would like to reorder the vector using break, but I do not know how.

 TIA
 Mark
 –––
 Mark Heckmann
 Dipl. Wirt.-Ing. cand. Psych.
 Vorstraße 93 B01
 28359 Bremen
 Blog: www.markheckmann.de
 R-Blog: http://ryouready.wordpress.com

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-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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Re: [R] Reordering the results from table(cut()) by break argument



On Dec 2, 2009, at 12:18 PM, Mark Heckmann wrote:

I have a vector and need to count how many data points fall inside  
each bin:


dat - rnorm(100)
breaks - -3:3
table((cut(dat, breaks)))

(-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
 3  13  42  30  12   0

if I reverse the breaks vector, the results remains the same:
breaks - rev(breaks)
table((cut(dat, breaks)))

(-3,-2] (-2,-1]  (-1,0]   (0,1]   (1,2]   (2,3]
 3  13  42  30  12   0

What I would like is break to also determine the order of the table  
output, in this case it should also be reversed, like:


Instead of reversing the breaks (which doesn't work because factors  
obey a very strange physics) reverse the table:


 rev(table((cut(dat, breaks

  (2,3]   (1,2]   (0,1]  (-1,0] (-2,-1] (-3,-2]
  2  21  25  35  14   3



( 3, 2] ( 2, 1]  ( 1,0]   (0,-1]   (-1,-2]   (-2,-3]
 0  12  30  42  13   3

Thus I would like to reorder the vector using break, but I do not  
know how.


TIA
Mark
–––
Mark Heckmann
Dipl. Wirt.-Ing. cand. Psych.
Vorstraße 93 B01
28359 Bremen
Blog: www.markheckmann.de
R-Blog: http://ryouready.wordpress.com

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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] R and eclipse

2009-12-02 Thread catuxa-2


   I found the eclipse plugin for R StatEt, hass anyone already worked with
it?
   It's posible to put inside of java code a R script with it?
   Thank you
-- 
View this message in context: 
http://n4.nabble.com/R-and-eclipse-tp934851p934851.html
Sent from the R help mailing list archive at Nabble.com.

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[R] Reading comments in text file from R

2009-12-02 Thread Graham Smith

When a text file starts with a few lines commented out with # can you
read those line from within R.

read.table ignores the comments to load the file, but it would
sometimes  be useful to be able to read what these comments say.

Thanks,

Graham

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Re: [R] Ridge regression

2009-12-02 Thread Ravi Varadhan

The help page clearly states that ans$coef is not on the original scale and
are for use by the coef method.  You also see that ans$scales gives you the
scales used in the computation of ans$coef.  

So, to get coefficients on the original scale, you can either use coef(ans)
or you can divide ans$coef by ans$scales.

X1 - runif(20)
X2 - runif(20)
Y - 2 * X1 - 2 * X2 + rnorm(20, sd=0.1)

lam - 10
ans1 - lm.ridge(Y ~ X1 + X2, lambda = lam)

all.equal(ans1$coef / ans1$scales, coef(ans1)[2:3] )

Hope this helps,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 





-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Ravi Varadhan
Sent: Wednesday, December 02, 2009 12:25 PM
To: 'David Winsemius'; 'Eleni Christodoulou'
Cc: r-help@r-project.org
Subject: Re: [R] Ridge regression

You are right that the ans$coef and coef(ans) are different in ridge
regression, where `ans' is the object from lm.ridge.  It is the coef(ans)
that yields the coefficients on the original scale.  ans$coef is the
coefficient of X-scaled and Y-centered version.

Here is an example that illustrates the workings of ridge regression.

First let us create some data:

X1 - runif(20)
X2 - runif(20)
Y - 2 * X1 - 2 * X2 + rnorm(20, sd=0.1)

lam - 10
ans1 - lm.ridge(Y ~ X1 + X2, lambda = lam)
ans1$coef
coef(ans1)
# Note that these two are different

# Now Let us scale the variables X1 and X2 and center Y
#
cY - scale(Y, scale=FALSE) 
n - length(Y)
sX1 - scale(X1) * sqrt(n/(n-1)) 
sX2 - scale(X2) *  sqrt(n/(n-1))

require(MASS)

lam - 10
ans2 - lm.ridge(cY ~ sX1 + sX2, lambda = lam)

ans2$coef
coef(ans2)
# Now, see that the coefficients of sX1 and sX2 are the same
# This is the connection!

# Armed with this insight, we now compare the ans1$coef with scaled
coefficients
#
ans1$coef
c(coef(ans1)[2] * sd(X1), coef(ans1)[3] * sd(X2)) * sqrt((n-1)/n)

# Now they are the same!

I hope this is clear.

Best,
Ravi.


---

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvarad...@jhmi.edu

Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h
tml

 




-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Winsemius
Sent: Wednesday, December 02, 2009 11:04 AM
To: Eleni Christodoulou
Cc: r-help@r-project.org
Subject: Re: [R] Ridge regression


On Dec 2, 2009, at 10:42 AM, Eleni Christodoulou wrote:

 Dear list,

 I have a couple of questions concerning ridge regression. I am using  
 the
 lm.ridge(...) function in order to fit a model to my microarray data.
 Thus *model=lm.ridge(...)*
 I retrieve some coefficients and some scales for each gene. First of  
 all, I
 would like to ask: the real coefficients of the model are not  
 included in
 the first argument of the output but in the result of coef(model),  
 am I
 right?

Not exactly. coef(model) extracts the coefficients from the model but  
the coefficients do in the example instance I created following the  
help page happen to be in the first element of the model.

eg:
  long.rr$coef
  GNP   Unemployed Armed.Forces   Population Year  
Employed
   25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825
  long.rr[[1]]
  GNP   Unemployed Armed.Forces   Population Year  
Employed
   25.36152883.30094160.7520553  -11.6992718   -6.5403380 
0.7864825

 Moreover, what does the scale argument represent? Which is its
 connection with the coefficients? The R help file os not very  
 informative
 for me...

A plausible response to such a question might be that the help page is  
a sketchy substitute for the MASS book. However, I cannot find ridge  
regression in the table of contents or in the index of my copy, but I  
only have ed. 2 and the current edition is the 4th. So we will both  
need to wait for more knowledgeable (or with more recent editions of  
MASS) persons to answer that question.

(And scales is not an argument, rather it's a returned value.)


 Thank you very much in advance,
 Eleni Christodoulou



David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Reading comments in text file from R